Contacts of the helix formed by residues 283 - 308 (chain A) in PDB entry 5Q1B
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 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 1.3 77.1 - - - +
284A ALA* 1.3 59.5 + - - +
285A GLU* 3.6 10.0 + - - +
286A GLU* 2.8 38.0 + - - +
287A ASN* 3.0 26.5 + - - -
358A ASN 5.7 0.2 - - - -
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A SER* 1.3 73.7 - - - +
285A GLU* 1.4 57.2 + - + +
287A ASN* 3.4 0.9 + - - +
288A PHE 2.9 23.6 + - - -
358A ASN 5.4 1.9 + - - +
359A SER 3.4 20.4 - - - +
360A GLY* 3.8 13.7 - - - -
458A TRP* 3.3 10.2 + - - -
459A ARG* 3.4 35.7 - - + +
460A VAL* 3.4 4.2 - - + +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A SER* 3.2 9.1 + - - +
284A ALA* 1.4 76.0 - - + +
286A GLU* 1.4 62.7 + - + +
288A PHE* 3.6 3.5 + - - +
289A LEU* 3.3 21.8 + - - +
459A ARG 5.2 1.3 - - - +
460A VAL* 3.6 19.3 - - + -
461A ASN* 3.1 47.7 + - - +
462A ASP 5.4 1.8 - - - -
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA 4.9 0.3 - - - +
282A PHE* 3.4 32.3 - - + -
283A SER* 2.8 39.1 + - - +
285A GLU* 1.4 75.5 - - + +
287A ASN* 1.4 56.4 + - - +
289A LEU* 3.4 9.3 + - - +
290A ILE* 3.0 33.6 + - + +
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Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 5.6 6.6 - - - +
282A PHE* 3.3 31.0 + - - +
283A SER 3.0 20.9 + - - +
284A ALA 3.6 0.2 - - - +
285A GLU 3.3 0.2 - - - -
286A GLU* 1.4 74.5 - - - +
288A PHE* 1.4 58.7 + - - +
290A ILE* 3.2 10.9 + - - +
291A LEU* 2.9 24.6 + - - +
355A ARG 4.9 3.0 + - - -
358A ASN 4.3 2.2 + - - -
359A SER* 3.3 42.2 + - - +
458A TRP* 4.4 2.5 - - + -
501A 9N7 3.4 28.4 - - + +
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA 2.9 16.9 + - - +
285A GLU 3.9 3.8 - - - +
286A GLU 3.5 0.2 - - - -
287A ASN* 1.4 74.4 - - - +
289A LEU* 1.4 59.1 + - - +
291A LEU* 3.2 10.8 + - + +
292A THR* 3.0 39.1 + - + +
455A LEU* 4.0 31.2 - - + -
458A TRP* 3.7 32.0 - + + +
460A VAL* 3.8 12.6 - - + -
462A ASP 4.4 8.1 - - - -
463A HIS* 3.8 15.0 - + + -
464A LYS* 3.5 33.4 - - + -
465A PHE* 3.7 27.8 - + - -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU 3.3 12.6 + - - +
286A GLU* 3.5 13.9 - - - +
288A PHE* 1.4 79.1 - - - +
290A ILE* 1.4 64.4 + - + +
292A THR* 2.9 25.7 + - - +
293A GLU* 3.1 15.8 + - + +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 4.4 24.9 - - + +
277A ILE* 5.1 8.7 - - + -
282A PHE* 3.8 40.8 - - + -
286A GLU* 3.0 25.0 + - + +
287A ASN* 3.5 12.3 - - - +
289A LEU* 1.4 75.6 - - + +
291A LEU* 1.4 52.9 + - - +
293A GLU* 3.2 7.4 + - - +
294A MET* 2.8 63.7 + - + +
501A 9N7 3.9 16.2 - - + +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASN 2.9 13.8 + - - +
288A PHE* 3.3 18.8 - - + +
290A ILE* 1.4 76.7 - - - +
292A THR* 1.3 56.0 + - + +
294A MET* 3.4 2.2 + - - +
295A ALA* 2.9 34.1 + - + +
332A MET* 4.6 12.3 - - + -
455A LEU* 3.8 28.9 - - + -
458A TRP* 4.0 25.8 - - + -
473A TRP* 4.3 6.1 - - + -
501A 9N7 3.8 60.8 - - + +
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PHE* 3.0 30.8 + - + +
289A LEU* 2.9 31.0 + - - +
291A LEU* 1.3 73.0 - - + +
293A GLU* 1.3 55.0 + - - +
295A ALA* 4.5 1.6 - - - -
296A THR* 2.6 38.1 + - - -
464A LYS 3.9 22.2 + - - +
465A PHE* 4.8 1.8 - - + -
466A THR* 5.5 6.5 - - - +
469A LEU* 3.4 23.3 - - + +
473A TRP* 4.5 11.2 - - + -
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG* 3.1 40.4 + - - -
276A LYS* 6.2 0.2 - - - -
289A LEU* 3.1 20.2 + - + +
290A ILE* 3.6 6.5 - - - +
292A THR* 1.3 73.9 + - - +
294A MET* 1.4 75.2 + - - +
296A THR* 3.3 6.4 + - - -
297A ASN* 3.2 20.1 + - - +
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG* 3.2 31.4 + - - +
272A GLU* 5.5 2.0 - - - +
273A ILE* 4.0 20.4 - - + +
276A LYS* 4.2 26.9 - - + -
277A ILE* 6.0 0.7 - - + -
290A ILE* 2.8 41.6 + - + +
291A LEU* 3.6 4.5 - - + +
293A GLU* 1.4 80.4 + - - +
295A ALA* 1.3 55.7 + - - +
297A ASN* 3.4 4.2 + - - +
298A HIS* 2.9 29.3 + - - +
501A 9N7 3.4 52.6 - - + +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 2.9 17.1 + - + +
292A THR 4.0 1.3 - - - +
294A MET* 1.3 72.7 - - - +
296A THR* 1.3 65.6 + - - +
298A HIS* 3.6 1.1 - - - +
299A VAL* 3.0 31.0 + - + +
332A MET* 3.7 24.6 - - + -
469A LEU* 3.8 6.3 - - + -
473A TRP* 3.5 35.2 - - + -
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR 2.6 24.3 + - - -
293A GLU* 3.3 7.2 + - - -
295A ALA* 1.3 76.5 - - - +
297A ASN* 1.4 60.7 + - - +
299A VAL* 3.5 3.9 + - - +
300A GLN* 3.2 43.0 + - - +
466A THR* 3.7 18.4 + - + +
468A LEU* 4.3 13.4 - - + +
469A LEU* 3.4 20.7 - - - +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG* 3.4 50.9 + - - +
293A GLU* 3.2 12.5 + - - +
294A MET 3.8 6.1 - - - +
296A THR* 1.4 74.1 - - - +
298A HIS* 1.4 58.8 + - - +
300A GLN* 3.2 17.9 + - - +
301A VAL* 2.9 43.8 + - - +
501A 9N7 4.1 6.6 - - - +
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Residues in contact with HIS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN* 4.3 14.2 + - - -
294A MET 2.9 18.1 + - - +
295A ALA* 3.6 9.0 - - - +
296A THR 3.4 0.4 - - - -
297A ASN* 1.4 75.7 + - - +
299A VAL* 1.3 67.4 + - + +
301A VAL* 3.3 5.9 + - - +
302A LEU* 2.9 38.1 + - + +
328A ALA 3.9 7.1 + - - -
331A ALA* 3.6 18.5 - - + +
332A MET* 3.3 50.4 + - + -
335A ARG* 4.2 9.2 - - + -
501A 9N7 3.4 29.8 + - - -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 3.0 20.3 + - + +
296A THR* 4.0 3.6 - - - +
298A HIS* 1.3 78.8 - - + +
300A GLN* 1.3 65.4 + - - +
302A LEU* 3.6 5.6 - - - +
303A VAL* 3.0 34.6 + - + +
324A LEU* 4.7 4.3 - - + -
328A ALA* 4.4 9.9 - - + +
332A MET* 6.2 1.6 - - + -
468A LEU* 4.7 15.5 - - + -
469A LEU* 4.8 5.4 - - + -
472A ILE* 3.6 49.8 - - + -
473A TRP* 5.8 0.7 - - - +
749B LEU* 4.7 4.5 - - + -
752B LEU* 5.7 0.2 - - + -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A THR* 3.2 33.1 + - - +
297A ASN* 3.2 21.4 + - - +
299A VAL* 1.3 78.5 - - - +
301A VAL* 1.3 61.5 + - + +
303A VAL* 3.4 9.2 + - - +
304A GLU* 3.5 17.7 + - - +
468A LEU* 3.8 18.2 - - + +
752B LEU* 4.4 18.1 - - + +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER 5.8 1.1 - - - +
266A LYS* 4.4 15.5 - - + +
267A GLN* 3.7 42.2 - - + +
268A ARG 5.3 2.2 - - - +
297A ASN* 2.9 36.8 + - - +
298A HIS* 3.9 5.6 - - - +
300A GLN* 1.3 74.3 - - + +
302A LEU* 1.4 57.5 + - - +
304A GLU* 3.3 9.8 + - + +
305A PHE* 3.0 28.9 + - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN* 5.6 4.9 - - - +
298A HIS* 2.9 31.2 + - + +
299A VAL* 3.6 7.2 - - - +
300A GLN 3.3 0.2 - - - -
301A VAL* 1.4 73.9 - - - +
303A VAL* 1.3 56.2 + - - +
305A PHE* 3.3 8.8 + - + +
306A THR* 2.7 44.2 + - - +
324A LEU* 4.5 12.3 - - + -
327A SER* 4.7 6.3 - - - +
328A ALA* 3.7 35.7 - - + +
331A ALA* 3.8 25.1 - - + -
390A THR* 4.3 9.0 - - + -
394A ILE* 3.9 20.0 - - + -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.0 26.7 + - + +
300A GLN 3.9 5.4 - - - +
301A VAL 3.4 0.6 - - - -
302A LEU* 1.3 72.6 - - - +
304A GLU* 1.3 60.9 + - - +
306A THR* 3.2 7.6 + - - -
307A LYS* 2.9 42.1 + - + +
324A LEU* 3.8 25.6 - - + -
749B LEU* 4.6 4.9 - - + -
752B LEU* 3.8 50.7 - - + +
753B LEU* 3.9 16.8 - - + -
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLN 3.5 11.0 + - - +
301A VAL* 3.3 11.7 + - - +
303A VAL* 1.3 79.8 - - - +
305A PHE* 1.4 60.1 + - - +
307A LYS* 3.6 23.1 + - - +
308A LYS* 3.3 51.0 + - - +
752B LEU* 4.5 2.1 - - - +
755B LYS* 3.3 26.1 + - - -
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 3.8 30.7 - - + -
263A SER* 3.8 16.9 - - - +
264A TYR* 3.8 34.5 - + - -
267A GLN* 6.5 0.9 - - + -
301A VAL* 3.0 17.0 + - + +
302A LEU* 3.3 12.1 + - + +
304A GLU* 1.4 74.9 - - - +
306A THR* 1.3 62.6 + - - +
308A LYS* 3.2 18.4 + - - +
309A LEU* 3.4 31.2 + - + +
387A ALA 3.7 21.8 - - - -
390A THR* 4.1 12.6 - - + -
391A ALA* 4.1 4.5 - - + -
394A ILE* 3.7 31.0 - - + -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 2.7 24.8 + - - +
303A VAL* 3.4 6.7 - - - +
305A PHE* 1.3 76.1 - - - +
307A LYS* 1.3 56.9 + - - +
309A LEU* 3.0 32.5 + - - +
312A PHE* 3.4 45.6 - - + +
324A LEU* 4.0 16.0 - - + +
394A ILE* 3.6 34.3 - - + +
753B LEU* 5.0 0.2 - - + -
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 2.9 28.1 + - + +
304A GLU* 3.6 31.6 + - - +
305A PHE 3.4 0.2 - - - -
306A THR* 1.3 71.6 - - - +
308A LYS* 1.3 60.3 + - + +
309A LEU 3.3 5.1 + - - +
312A PHE* 4.2 3.1 - - - +
313A GLN* 3.0 47.3 + - - +
752B LEU 3.0 24.8 + - - +
753B LEU* 3.7 33.4 - - + +
755B LYS* 3.0 32.2 + - - +
756B ASP* 4.9 2.4 - - - +
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 3.1 36.2 - - + -
260A ILE* 5.7 0.7 - - - -
263A SER* 3.4 32.8 - - - +
266A LYS* 5.7 11.2 - - - +
304A GLU* 3.3 42.6 + - - +
305A PHE* 3.2 9.7 + - - +
306A THR 3.2 1.0 - - - -
307A LYS* 1.3 76.6 - - + +
309A LEU* 1.4 64.1 + - - +
310A PRO* 3.4 1.9 - - - +
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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