Contacts of the helix formed by residues 319 - 347 (chain A) in PDB entry 1YNU
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 ASP 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 2.9 31.7 + - + +
62A ASN* 5.3 1.2 - - - +
315A ALA 3.4 7.1 + - - +
316A MET 3.2 10.6 + - - +
318A SER* 1.3 73.4 - - - +
320A LYS* 1.3 58.0 + - - +
321A LYS* 3.0 26.9 + - - +
322A LEU* 2.9 29.7 + - + +
323A THR* 3.0 15.5 + - - +
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Residues in contact with LYS 320 (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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97A ASP* 3.9 32.4 + - - +
98A PHE* 5.3 1.0 - - - +
101A GLU* 4.3 23.6 + - - +
317A LEU 4.6 12.5 + - - -
318A SER* 3.0 14.3 + - - +
319A ASP* 1.3 70.7 + - - +
321A LYS* 1.3 58.4 + - + +
322A LEU 3.4 0.2 - - - -
323A THR* 3.5 6.6 + - - +
324A LYS* 3.2 30.1 + - - +
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Residues in contact with LYS 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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319A ASP* 3.0 12.0 + - - +
320A LYS* 1.3 76.7 - - + +
322A LEU* 1.3 65.7 + - - +
324A LYS* 4.1 4.1 - - - +
325A ASN* 3.2 25.5 + - - +
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Residues in contact with LEU 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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54A LEU* 4.2 20.2 - - + +
55A LEU* 4.6 11.7 - - + -
58A TRP* 3.7 43.1 - - + +
316A MET* 3.7 35.7 - - + +
319A ASP* 2.9 21.1 + - + +
321A LYS* 1.3 81.2 - - - +
323A THR* 1.3 60.6 + - + +
325A ASN* 3.7 6.4 - - - +
326A TYR* 2.8 36.3 + - + +
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Residues in contact with THR 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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98A PHE* 4.2 15.5 - - + -
101A GLU* 2.8 25.9 + - - -
316A MET 4.0 3.1 - - - +
317A LEU* 3.9 43.9 + - + +
319A ASP 3.0 9.2 + - - +
320A LYS* 3.5 18.0 + - - +
322A LEU* 1.3 75.4 - - + +
324A LYS* 1.3 65.5 + - - +
326A TYR* 4.2 5.2 - - - -
327A ILE* 3.0 32.3 + - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU* 4.1 17.5 - - - +
320A LYS 3.2 17.3 + - - +
321A LYS* 4.1 4.5 - - - +
323A THR* 1.3 80.2 + - - +
325A ASN* 1.3 62.7 + - - +
327A ILE* 4.0 3.1 - - - +
328A ALA* 3.3 24.6 + - + +
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Residues in contact with ASN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.2 20.4 - - - +
321A LYS 3.2 17.1 + - - +
322A LEU* 3.9 6.1 - - + +
324A LYS* 1.3 78.9 - - - +
326A TYR* 1.3 64.5 + - - +
328A ALA* 4.7 4.8 - - - +
329A GLU* 3.0 34.6 + - - +
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Residues in contact with TYR 326 (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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48A ASN* 4.4 4.2 + - - -
51A CYS* 3.3 42.8 - - + +
54A LEU* 4.1 16.4 - - + +
55A LEU* 4.0 28.7 - - + -
98A PHE* 5.6 1.8 - + + -
274A ASP* 2.6 31.6 + - + -
275A LEU* 3.4 33.6 + - + -
276A GLY* 5.1 0.2 - - - -
322A LEU* 2.8 23.9 + - + +
323A THR* 3.3 7.6 + - - +
325A ASN* 1.3 77.5 + - - +
327A ILE* 1.3 67.8 + - + +
329A GLU* 3.7 0.7 - - - +
330A ASN* 2.8 50.6 + - + +
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Residues in contact with ILE 327 (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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98A PHE* 3.9 25.1 - - + -
101A GLU* 3.5 35.2 - - + +
102A ILE* 4.3 17.0 - - + +
235A GLY* 5.4 4.3 - - - +
323A THR 3.0 17.6 + - - +
324A LYS* 4.0 3.8 - - - +
326A TYR* 1.3 83.9 - - + +
328A ALA* 1.3 63.1 + - - +
330A ASN* 3.3 4.0 + - - +
331A HIS* 3.1 50.2 + - + +
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Residues in contact with ALA 328 (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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324A LYS* 3.3 16.8 + - + +
325A ASN* 4.1 6.3 - - - +
327A ILE* 1.3 79.6 - - - +
329A GLU* 1.3 62.5 + - - +
331A HIS* 3.5 7.5 + - - +
332A LYS* 3.3 22.6 + - - +
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Residues in contact with GLU 329 (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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51A CYS* 4.2 1.1 - - - -
54A LEU* 3.7 21.1 - - + -
325A ASN* 3.0 29.2 + - - +
328A ALA* 1.3 75.1 - - - +
330A ASN* 1.3 61.5 + - - +
332A LYS* 3.6 22.1 + - - +
333A ARG* 2.8 80.1 + - - +
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Residues in contact with ASN 330 (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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48A ASN* 2.9 32.8 + - - +
50A LEU* 4.8 1.0 - - - +
51A CYS* 3.3 24.4 - - - -
235A GLY 3.9 13.7 + - - -
236A THR* 4.9 0.4 - - - +
274A ASP* 3.5 16.6 + - - +
326A TYR* 2.8 35.2 + - + +
327A ILE* 3.7 5.1 - - - +
329A GLU* 1.3 71.4 - - - +
331A HIS* 1.3 59.8 + - + +
333A ARG* 3.3 1.4 + - - +
334A LEU* 2.8 50.5 + - - +
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Residues in contact with HIS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLY* 3.4 29.7 + - - -
236A THR* 4.7 1.6 - - - -
237A ALA* 3.4 31.5 + - + +
238A PHE* 3.2 22.4 - - + +
327A ILE* 3.1 39.7 + - + +
328A ALA* 3.8 6.9 - - - +
329A GLU 3.4 0.2 - - - -
330A ASN* 1.3 76.0 - - + +
332A LYS* 1.3 58.4 + - - +
334A LEU* 4.4 1.1 - - + -
335A LYS* 2.9 29.3 + - - +
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Residues in contact with LYS 332 (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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328A ALA 3.3 14.8 + - - +
329A GLU* 3.7 27.5 + - - +
330A ASN 3.2 0.2 - - - -
331A HIS* 1.3 80.5 - - - +
333A ARG* 1.3 59.3 + - + +
335A LYS* 3.4 5.6 + - - +
336A GLN* 3.0 44.4 + - + +
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Residues in contact with ARG 333 (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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50A LEU* 2.8 53.9 + - + +
51A CYS* 3.9 9.5 - - - +
53A ASP* 2.9 33.1 + - - -
54A LEU* 4.0 9.6 - - - +
329A GLU* 2.8 54.4 + - - +
330A ASN* 4.0 3.1 - - - +
332A LYS* 1.3 74.8 - - + +
334A LEU* 1.3 61.2 + - - +
336A GLN* 3.4 10.8 + - - +
337A ARG* 2.9 31.4 + - - +
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Residues in contact with LEU 334 (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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48A ASN* 4.0 7.4 - - - +
50A LEU* 3.9 19.3 - - + -
235A GLY 4.7 0.2 - - - +
236A THR* 3.8 30.3 - - + -
238A PHE* 3.6 18.6 - - + -
330A ASN* 2.8 48.2 + - - +
331A HIS* 3.6 7.4 - - - +
333A ARG* 1.3 77.5 - - - +
335A LYS* 1.3 52.1 + - - +
337A ARG* 3.1 3.1 + - - +
338A GLN* 2.7 36.9 + - - +
358A GLY 4.5 1.8 - - - +
359A LEU* 3.7 23.6 - - + -
410A PHE* 4.0 9.5 - - + -
411A ALA* 4.3 6.7 - - + -
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Residues in contact with LYS 335 (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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238A PHE* 3.7 26.8 - - + +
239A SER* 3.7 21.7 + - - +
331A HIS 2.9 17.6 + - - +
332A LYS* 3.7 5.8 - - - +
334A LEU* 1.3 75.9 - - - +
336A GLN* 1.3 63.5 + - - +
338A GLN* 3.1 3.4 + - - +
339A LYS* 3.1 51.5 + - + +
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Residues in contact with GLN 336 (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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332A LYS* 3.0 35.5 + - - +
333A ARG* 3.8 10.4 - - - +
335A LYS* 1.3 80.0 - - - +
337A ARG* 1.3 64.3 + - - +
339A LYS* 3.5 10.8 + - - +
340A LYS* 3.3 20.0 + - + +
415A GLU* 4.4 14.2 - - - +
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Residues in contact with ARG 337 (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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50A LEU* 3.3 37.2 - - + +
333A ARG 2.9 18.6 + - - +
334A LEU 3.5 3.4 - - - +
336A GLN* 1.3 77.2 - - - +
338A GLN* 1.3 63.9 + - - +
340A LYS* 3.3 7.9 + - - +
341A LEU* 3.3 18.9 + - - +
410A PHE* 2.8 53.7 + - + +
411A ALA* 4.1 1.6 - - - +
413A LEU* 2.9 32.1 + - - +
414A PRO* 4.5 0.8 - - - +
415A GLU* 3.5 39.4 + - - +
418A LEU* 3.4 25.3 - - - +
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Residues in contact with GLN 338 (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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238A PHE* 3.7 26.0 - - + -
334A LEU 2.7 19.4 + - - +
335A LYS* 3.1 5.2 + - - +
337A ARG* 1.3 72.8 - - - +
339A LYS* 1.3 75.8 + - - +
341A LEU* 3.0 14.2 + - - +
342A VAL* 3.0 27.0 + - - +
354A ASN* 5.9 0.4 - - - +
355A GLY* 2.8 37.2 + - - +
360A PHE 5.6 0.4 + - - +
361A CYS* 4.0 13.7 - - - -
410A PHE* 3.8 29.8 - - + -
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Residues in contact with LYS 339 (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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335A LYS* 3.1 49.0 + - + +
336A GLN* 3.9 7.4 - - - +
338A GLN* 1.3 85.7 - - - +
340A LYS* 1.3 58.8 + - - +
342A VAL* 3.7 6.5 - - + +
343A SER* 2.8 33.8 + - - -
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Residues in contact with LYS 340 (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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336A GLN* 3.3 11.7 + - + +
337A ARG* 3.5 13.2 - - - +
338A GLN 3.2 0.4 - - - -
339A LYS* 1.3 78.7 - - - +
341A LEU* 1.3 60.4 + - - +
343A SER* 4.7 4.9 - - - -
344A GLY* 3.2 18.5 + - - +
415A GLU* 3.9 27.5 + - + +
418A LEU* 4.4 16.2 - - + +
419A ASP* 2.7 38.4 + - - +
422A MET* 5.0 3.6 - - - +
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Residues in contact with LEU 341 (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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337A ARG 3.3 7.6 + - - +
338A GLN 3.0 10.0 + - - +
340A LYS* 1.3 78.1 - - - +
342A VAL* 1.3 55.7 + - - +
344A GLY* 3.1 1.3 + - - -
345A LEU* 2.8 51.5 + - + +
361A CYS* 3.8 31.9 - - + -
408A VAL* 3.9 28.5 - - + +
410A PHE* 3.8 23.8 - - + -
418A LEU* 4.2 18.8 - - + +
422A MET* 3.8 29.4 - - + -
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Residues in contact with VAL 342 (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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338A GLN* 3.0 37.6 + - - +
339A LYS* 3.7 8.7 - - - +
341A LEU* 1.3 75.4 - - - +
343A SER* 1.3 53.0 + - - +
345A LEU* 3.1 10.6 + - - +
346A GLN* 2.7 61.4 + - + +
350A ILE 4.6 0.2 - - - +
352A CYS* 4.8 16.2 - - + +
361A CYS* 4.3 13.2 - - - -
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LYS 2.8 17.5 + - - -
340A LYS* 4.4 7.2 - - - -
342A VAL* 1.3 73.2 - - - +
344A GLY* 1.3 66.0 + - - +
346A GLN* 3.3 18.9 + - - +
347A LYS* 3.0 22.5 + - - +
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Residues in contact with GLY 344 (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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340A LYS* 3.2 13.3 + - - +
341A LEU 3.1 7.5 + - - -
343A SER* 1.3 78.4 + - - +
345A LEU* 1.3 58.0 + - - +
347A LYS* 2.7 41.5 + - - +
348A SER* 3.7 1.2 + - - -
422A MET* 3.7 23.1 - - - +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 2.8 36.8 + - + +
342A VAL 3.4 6.5 - - - +
344A GLY* 1.3 72.7 - - - +
346A GLN* 1.3 53.7 + - - +
347A LYS 2.9 4.9 - - - -
348A SER* 2.8 27.4 + - - +
350A ILE* 2.9 37.7 + - + +
352A CYS* 3.1 33.2 - - - -
363A VAL* 3.7 20.2 - - + -
408A VAL* 5.6 4.9 - - + -
422A MET* 4.2 10.3 - - + -
425A LEU* 3.6 28.3 - - + -
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Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A VAL* 2.7 47.3 + - + +
343A SER* 3.3 18.9 + - - +
345A LEU* 1.3 72.8 - - - +
347A LYS* 1.3 55.4 + - - +
349A GLY* 2.8 19.6 + - - -
350A ILE 3.4 14.6 + - - +
351A SER* 5.8 2.0 - - - -
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER 3.0 11.8 + - - +
344A GLY* 2.7 42.0 + - - +
345A LEU 2.9 0.2 - - - -
346A GLN* 1.3 78.3 - - - +
348A SER* 1.3 67.0 + - - +
349A GLY 3.2 0.7 - - - -
422A MET* 3.5 25.8 + - - +
423A GLN* 4.9 5.4 - - - +
426A LYS* 2.7 53.7 + - + +
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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