Contacts of the helix formed by residues 305 - 338 (chain A) in PDB entry 3QMK
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 305 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 4.1 1.5 - - - +
302A GLY 5.4 0.4 - - - -
303A GLU 3.9 2.2 + - - -
304A ILE* 1.3 78.8 - - - +
306A GLU* 1.3 64.3 + - - +
307A HIS* 3.5 8.3 + - - +
308A GLU* 3.0 34.2 + - - +
309A GLY* 3.0 19.6 + - - -
1C SGN 5.6 3.6 - - - -
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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
----------------------------------------------------------
300A MET* 4.3 10.5 - - - +
305A SER* 1.3 73.6 - - - +
307A HIS* 1.3 59.0 + - - +
309A GLY 3.4 0.3 + - - -
310A PHE* 2.9 32.6 + - - +
375A THR* 5.3 0.5 - - - +
376A HIS* 2.7 43.4 + - + +
379A ARG* 2.9 53.4 + - + -
380A VAL* 4.7 7.9 - - + +
383A LEU* 5.2 12.3 - - + +
1C SGN 5.1 6.5 + - - +
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Residues in contact with HIS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER* 3.2 7.7 + - - +
306A GLU* 1.3 81.6 - - - +
308A GLU* 1.3 61.1 + - + +
310A PHE* 3.4 5.6 - + - +
311A LEU* 3.1 56.1 + - + +
376A HIS* 4.2 18.1 + - + -
1C SGN 3.5 72.9 + - - +
2C IDS 3.1 41.4 + - - -
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU 3.9 6.1 - - - +
304A ILE* 3.5 25.2 - - + -
305A SER* 3.0 31.6 + - - +
307A HIS* 1.3 81.3 - - + +
309A GLY* 1.3 66.4 + - - +
311A LEU* 3.9 10.0 - - + +
312A ARG* 3.0 24.9 + - - +
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Residues in contact with GLY 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 3.6 31.8 - - - +
304A ILE* 3.9 6.1 - - - -
305A SER 3.0 13.4 + - - -
306A GLU 3.9 0.7 - - - -
308A GLU* 1.3 77.7 - - - +
310A PHE* 1.3 63.0 + - - +
312A ARG* 3.3 7.3 + - - +
313A ALA* 2.9 24.8 + - - +
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Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 5.1 0.2 - - - -
306A GLU* 2.9 22.6 + - - +
307A HIS* 3.4 8.5 - + - +
309A GLY* 1.3 74.6 - - - +
311A LEU* 1.3 70.9 + - + +
313A ALA* 3.2 7.9 + - - +
314A LYS* 2.8 49.1 + - + +
372A LEU* 3.9 37.0 - - + +
373A VAL* 4.5 9.6 - - + -
376A HIS* 3.5 55.0 - + + +
2C IDS 5.9 1.3 - - - -
3C SGN 6.2 0.9 - - - -
4C IDS 3.3 29.4 - - - -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A HIS* 3.1 49.3 + - + +
308A GLU* 4.0 8.1 - - + +
309A GLY 3.4 0.2 - - - -
310A PHE* 1.3 93.4 - - + +
312A ARG* 1.3 52.6 + - - +
314A LYS* 3.2 24.3 + - - +
315A MET* 2.8 36.7 + - - +
1C SGN 4.9 4.0 - - - +
2C IDS 5.1 4.3 - - - +
4C IDS 5.7 0.2 - - - +
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU 3.0 19.5 + - - +
309A GLY* 3.4 7.4 - - - +
311A LEU* 1.3 75.5 - - - +
313A ALA* 1.3 58.4 + - - +
315A MET* 3.2 28.0 + - - +
316A ASP* 2.9 60.9 + - - +
319A GLU* 5.0 5.7 + - - -
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLY 2.9 12.8 + - - +
310A PHE* 3.4 9.2 - - - +
312A ARG* 1.3 76.8 - - - +
314A LYS* 1.3 64.1 + - - +
316A ASP* 3.3 8.4 + - - +
317A LEU* 3.0 30.8 + - + +
372A LEU* 4.1 20.0 - - + -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 2.8 47.5 + - + +
311A LEU* 3.5 21.2 - - - +
313A ALA* 1.3 75.6 - - - +
315A MET* 1.3 57.9 + - - +
317A LEU* 3.4 3.9 + - - +
318A GLU* 3.0 28.3 + - + +
369A ARG* 3.7 37.4 + - - +
372A LEU* 3.7 18.3 - - + +
4C IDS 3.2 35.9 + - - +
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Residues in contact with MET 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU 2.8 17.1 + - - +
312A ARG* 3.4 28.0 - - - +
314A LYS* 1.3 74.7 - - - +
316A ASP* 1.3 66.0 + - - +
318A GLU* 3.1 38.7 + - - +
319A GLU* 3.1 56.9 + - + +
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 2.9 50.0 + - - +
313A ALA* 3.7 7.5 - - - +
315A MET* 1.3 76.2 - - - +
317A LEU* 1.3 65.9 + - + +
319A GLU* 3.4 10.9 + - - +
320A ARG* 3.0 32.4 + - - +
323A ARG* 5.1 1.2 + - - -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA* 3.0 21.9 + - + +
314A LYS* 3.7 4.5 - - - +
316A ASP* 1.3 78.5 - - + +
318A GLU* 1.3 57.5 + - - +
320A ARG* 3.2 33.5 + - - +
321A ARG* 2.9 36.5 + - - +
368A GLU* 3.2 51.4 - - + +
369A ARG* 5.9 0.7 - - - -
372A LEU* 4.1 25.8 - - + -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS* 3.0 16.8 + - + +
315A MET* 3.1 33.5 + - + +
317A LEU* 1.3 76.9 - - - +
319A GLU* 1.3 57.1 + - - +
321A ARG* 3.9 1.8 - - - +
322A MET* 2.9 41.2 + - - +
369A ARG* 5.6 3.5 + - - +
429B ARG* 3.6 33.7 + - - +
432B GLN* 3.6 35.4 + - - +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 5.0 4.1 + - - -
315A MET* 3.1 43.0 + - + +
316A ASP* 3.9 12.5 - - - +
318A GLU* 1.3 73.3 - - + +
320A ARG* 1.3 69.0 + - - +
322A MET* 3.4 9.9 + - - +
323A ARG* 3.1 41.1 + - - +
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP* 3.0 24.7 + - - +
317A LEU* 3.2 34.5 + - - +
319A GLU* 1.3 76.5 - - - +
321A ARG* 1.3 70.2 + - - +
323A ARG* 2.9 38.6 + - - +
324A GLN* 3.0 34.4 + - + +
368A GLU* 4.2 4.8 + - - -
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU 2.9 23.8 + - - +
318A GLU 4.1 2.5 - - - +
320A ARG* 1.3 78.7 - - + +
322A MET* 1.3 59.4 + - - +
324A GLN* 2.9 37.0 + - - +
325A ILE* 2.8 36.9 + - + +
361A LEU* 3.7 7.0 - - + +
364A GLN* 2.9 43.3 + - - +
365A VAL* 3.7 28.5 - - + +
368A GLU* 2.9 43.5 + - - +
432B GLN* 4.4 11.0 - - + -
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Residues in contact with MET 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 2.9 38.7 + - - +
319A GLU* 3.6 11.0 - - - +
320A ARG 3.2 0.2 - - - -
321A ARG* 1.3 76.6 - - - +
323A ARG* 1.3 58.1 + - + +
325A ILE* 3.8 7.2 - - - +
326A ASN* 3.0 29.6 + - - +
425B ARG* 3.7 42.6 - - + +
428B LEU* 4.3 22.2 - - + +
429B ARG* 3.8 36.3 - - + +
432B GLN* 4.3 9.0 - - + -
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Residues in contact with ARG 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP 5.1 1.0 + - - -
319A GLU* 3.1 35.9 + - - +
320A ARG* 2.9 33.2 + - - +
322A MET* 1.3 75.0 - - + +
324A GLN* 1.3 67.2 + - + +
326A ASN* 3.2 7.6 + - - +
327A GLU* 3.0 30.8 + - - +
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Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ARG* 3.0 40.5 + - + +
321A ARG* 2.9 44.3 + - - +
323A ARG* 1.3 76.9 - - + +
325A ILE* 1.3 64.4 + - - +
327A GLU* 3.1 17.7 + - - +
328A VAL* 3.1 16.2 + - + +
361A LEU* 3.2 22.1 - - + +
364A GLN* 4.5 0.9 - - - +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG* 2.8 24.8 + - + +
322A MET* 3.8 5.4 - - - +
324A GLN* 1.3 77.8 - - - +
326A ASN* 1.3 63.0 + - - +
328A VAL* 3.2 5.6 + - - +
329A MET* 2.9 30.2 + - + +
358A LEU* 5.0 2.5 - - + -
361A LEU* 3.5 27.4 - - + -
362A GLU* 6.5 0.4 - - + -
365A VAL* 5.1 5.4 - - + -
428B LEU* 3.8 21.1 - - + +
431B TYR* 3.8 39.9 - - + -
432B GLN* 4.2 25.1 - - + -
435B ALA* 6.1 2.2 - - + -
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Residues in contact with ASN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A MET 3.0 18.6 + - - +
323A ARG* 3.2 8.0 + - - +
325A ILE* 1.3 76.3 - - - +
327A GLU* 1.3 63.3 + - - +
329A MET* 3.4 3.1 + - - +
330A ARG* 2.8 35.7 + - - +
424B GLN* 2.8 31.4 + - - +
428B LEU* 3.5 22.6 - - + +
453B LEU* 4.9 4.3 - - - +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 3.0 19.5 + - - +
324A GLN* 3.1 13.2 + - - +
326A ASN* 1.3 81.5 + - - +
328A VAL* 1.3 64.9 + - + +
330A ARG* 3.1 10.0 + - - +
331A GLU* 2.9 31.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN* 3.1 11.9 + - + +
325A ILE 3.7 5.8 - - - +
327A GLU* 1.3 76.5 - - + +
329A MET* 1.3 58.1 + - - +
331A GLU* 3.2 12.4 + - - +
332A TRP* 2.8 28.5 + - + +
354A PHE* 4.0 15.9 - - + +
357A ILE* 3.7 31.4 - - + -
358A LEU* 3.5 37.0 - - + -
361A LEU* 4.5 7.4 - - + -
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Residues in contact with MET 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 2.9 26.4 + - + +
326A ASN* 3.7 5.4 - - - +
328A VAL* 1.3 76.7 - - - +
330A ARG* 1.3 61.6 + - - +
332A TRP* 3.4 14.6 + - - +
333A ALA* 3.0 22.5 + - - +
358A LEU* 3.7 22.9 - - + -
431B TYR* 3.9 19.7 - - + -
446B ARG 3.9 13.7 - - - +
449B VAL* 3.8 24.5 - - + -
450B HIS* 3.7 33.3 + - - +
453B LEU* 3.6 27.1 - - + -
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASN* 2.8 23.4 + - - +
327A GLU* 3.5 11.7 - - - +
329A MET* 1.3 75.8 - - - +
331A GLU* 1.3 59.4 + - - +
333A ALA* 3.1 8.4 + - - +
334A MET* 3.0 28.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLU* 2.9 18.4 + - + +
328A VAL* 3.5 16.5 - - - +
330A ARG* 1.3 74.9 - - - +
332A TRP* 1.3 60.6 + - - +
334A MET* 3.4 7.0 + - - +
335A ALA* 2.9 29.1 + - - +
353A HIS* 5.4 4.0 - - - -
354A PHE* 3.7 22.8 - - + -
357A ILE* 5.6 4.4 - - - +
----------------------------------------------------------
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Residues in contact with TRP 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A VAL 2.8 17.2 + - - +
329A MET* 3.6 9.4 - - - +
331A GLU* 1.3 76.9 - - - +
333A ALA* 1.3 62.5 + - - +
335A ALA* 3.4 1.1 + - + +
336A ASP* 3.1 34.9 + - - -
350A LEU* 5.6 1.1 - - + -
351A ASN* 3.7 33.0 - - - +
354A PHE* 3.4 40.9 - + + +
355A GLN* 3.8 28.0 - - + -
358A LEU* 3.8 30.7 - - + -
446B ARG* 4.5 5.8 - - + -
447B PHE* 4.0 13.2 - + - -
450B HIS* 3.5 50.1 + + + -
----------------------------------------------------------
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET 3.0 13.9 + - - +
330A ARG* 3.1 12.1 + - - +
332A TRP* 1.3 74.4 - - - +
334A MET* 1.3 65.5 + - - +
336A ASP* 3.1 13.7 + - - +
337A ASN* 3.2 13.2 + - - +
450B HIS* 3.9 2.7 - - + -
454B GLN* 4.0 32.6 + - + +
----------------------------------------------------------
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Residues in contact with MET 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG 3.0 13.3 + - - +
331A GLU* 3.7 9.6 - - - +
333A ALA* 1.3 76.1 - - - +
335A ALA* 1.3 62.7 + - - +
337A ASN* 3.3 8.5 + - - +
338A GLN* 3.1 42.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU 2.9 17.9 + - - +
332A TRP* 3.5 3.6 - - + +
333A ALA 3.1 0.2 - - - -
334A MET* 1.3 74.2 - - - +
336A ASP* 1.3 68.7 + - - +
338A GLN* 3.4 6.4 + - - +
339A SER* 3.0 25.6 + - - -
350A LEU* 5.2 7.9 - - + -
354A PHE* 3.4 28.9 - - + -
----------------------------------------------------------
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Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A TRP* 3.1 24.4 + - - +
333A ALA 3.1 7.2 + - - +
335A ALA* 1.3 76.6 - - - +
337A ASN* 1.3 59.6 + - - +
339A SER* 2.9 23.1 + - - -
340A LYS* 3.1 12.8 + - - +
350A LEU* 5.6 5.1 - - - +
351A ASN* 5.9 0.3 + - - -
450B HIS* 3.1 26.5 + - - -
454B GLN* 3.4 14.9 + - - +
----------------------------------------------------------
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Residues in contact with ASN 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA 3.2 9.1 + - - +
334A MET* 3.5 11.9 - - - +
336A ASP* 1.3 80.7 - - - +
338A GLN* 1.3 62.3 + - + +
339A SER 3.3 3.1 + - - -
340A LYS* 3.7 14.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A MET* 3.1 32.8 + - - +
335A ALA* 3.6 4.6 - - - +
336A ASP 3.3 0.2 - - - -
337A ASN* 1.3 80.7 - - + +
339A SER* 1.3 58.5 + - - +
341A ASN* 5.0 4.0 + - - +
342A LEU* 5.6 0.7 - - - +
----------------------------------------------------------
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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