Contacts of the helix formed by residues 310 - 331 (chain A) in PDB entry 1Y0S
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 PHE 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A SER 5.5 1.1 - - - -
309A LEU* 1.3 74.7 - - - +
311A LEU* 1.3 69.2 + - - +
312A ASN* 2.9 19.5 - - - +
313A ASP* 2.8 19.5 + - + +
314A GLN* 3.1 8.8 + - - +
401A MET* 3.7 25.1 - - + -
402A ASN* 6.0 4.0 - - + -
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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
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309A LEU 3.5 2.2 + - - -
310A PHE* 1.3 74.4 - - - +
312A ASN* 1.3 62.9 + - - +
314A GLN* 3.2 30.4 + - + +
315A VAL* 3.1 33.0 + - + +
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Residues in contact with ASN 312 (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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310A PHE* 2.9 26.9 - - - +
311A LEU* 1.3 75.8 + - - +
313A ASP* 1.3 67.9 + - - +
315A VAL* 3.3 9.2 + - - +
316A THR* 3.1 24.4 + - - -
401A MET* 3.4 30.9 - - - +
483A B7G 6.4 1.8 - - - -
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 4.6 17.1 - - + +
310A PHE 2.8 14.7 + - - +
312A ASN* 1.3 78.0 + - - +
314A GLN* 1.3 66.4 + - - +
316A THR* 3.0 7.2 + - - -
317A LEU* 2.9 29.0 + - - +
399A GLY 4.2 2.3 - - - +
400A LEU* 3.8 14.3 - - + +
401A MET* 2.8 43.4 + - - +
402A ASN* 2.9 32.8 + - - +
406A VAL* 5.3 0.6 - - + +
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Residues in contact with GLN 314 (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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301A LYS* 4.3 12.1 - - - +
306A PHE* 3.5 52.5 + - + +
307A SER* 3.2 20.3 + - - +
309A LEU* 2.8 27.2 + - + +
310A PHE 3.1 6.3 + - - +
311A LEU* 3.2 33.9 + - + +
313A ASP* 1.3 76.8 - - - +
315A VAL* 1.3 63.5 + - + +
317A LEU* 3.2 3.7 + - - +
318A LEU* 3.0 30.3 + - + +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 3.1 21.0 + - + +
312A ASN* 3.6 9.4 - - - +
313A ASP 3.2 0.2 - - - -
314A GLN* 1.3 77.6 - - + +
316A THR* 1.3 57.4 + - - +
318A LEU* 3.9 7.9 - - + +
319A LYS* 2.8 32.5 + - + +
483A B7G 3.8 64.8 - - + +
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Residues in contact with THR 316 (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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312A ASN 3.1 14.3 + - - -
313A ASP* 3.0 14.6 + - - -
315A VAL* 1.3 76.2 - - - +
317A LEU* 1.3 64.6 + - - +
319A LYS* 3.5 7.2 + - - +
320A TYR* 3.2 30.7 + - + +
397A ARG* 4.1 8.1 - - + -
398A PRO 3.4 26.2 + - - +
399A GLY* 4.4 7.4 + - - -
400A LEU* 3.9 22.9 - - + +
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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
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306A PHE* 4.0 14.8 - - + -
309A LEU* 3.8 29.6 - - + -
313A ASP 2.9 15.8 + - - +
314A GLN 3.7 5.6 - - - +
316A THR* 1.3 76.8 - - - +
318A LEU* 1.3 56.5 + - - +
320A TYR* 3.8 0.5 - - - +
321A GLY* 2.8 28.6 + - - -
392A ILE* 3.3 37.2 - - + +
393A LEU* 4.3 3.8 - - + -
394A CYS 3.5 26.0 - - - +
397A ARG* 3.8 10.0 + - + -
400A LEU* 3.7 20.0 - - + -
406A VAL* 4.1 13.2 - - + -
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Residues in contact with LEU 318 (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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296A LEU* 4.1 18.6 - - + +
297A THR* 3.5 35.0 - - + +
300A ALA* 4.2 11.2 - - + -
306A PHE* 4.3 11.4 - - + -
314A GLN* 3.0 23.5 + - + +
315A VAL* 3.9 2.0 - - + +
317A LEU* 1.3 74.6 - - - +
319A LYS* 1.3 66.1 + - - +
321A GLY 5.2 0.2 - - - -
322A VAL* 3.0 52.2 + - + +
392A ILE* 4.4 13.2 - - + -
483A B7G 3.6 27.6 - - + -
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Residues in contact with LYS 319 (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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315A VAL* 2.8 20.8 + - + +
316A THR* 3.7 7.2 - - - +
318A LEU* 1.3 77.9 - - - +
320A TYR* 1.3 96.3 + - + +
322A VAL* 4.5 2.3 - - - +
323A HIS* 5.2 0.9 + - - -
471A GLU 3.2 12.7 + - - -
472A ILE* 3.0 61.5 + - - +
474A LYS* 4.6 0.2 - - - +
475A ASP* 3.8 20.8 - - - +
483A B7G 3.8 50.1 + - + +
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Residues in contact with TYR 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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316A THR* 3.2 25.7 + - + +
317A LEU 3.8 0.2 - - - -
319A LYS* 1.3 109.1 - - + +
321A GLY* 1.3 59.3 + - - +
322A VAL 3.8 0.2 - - - -
323A HIS* 5.3 2.0 + - - +
324A GLU* 4.0 6.6 + - - +
397A ARG* 3.2 36.9 + - + +
398A PRO* 3.6 53.0 - - + +
446A VAL* 5.7 3.6 - - - +
472A ILE 5.3 2.5 - - - -
475A ASP 2.4 32.7 + - - -
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Residues in contact with GLY 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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317A LEU 2.8 17.8 + - - -
320A TYR* 1.3 79.2 - - - +
322A VAL* 1.3 64.7 + - - +
323A HIS 3.4 2.9 - - - -
324A GLU* 3.2 8.2 + - - +
325A ALA* 3.0 19.3 + - - +
391A ILE* 3.6 10.4 - - - +
392A ILE* 5.1 6.1 - - - -
397A ARG* 3.8 17.7 - - - -
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Residues in contact with VAL 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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293A VAL* 4.4 24.9 - - + -
296A LEU* 3.8 27.1 - - + -
318A LEU* 3.0 48.1 + - + +
319A LYS 4.5 2.5 - - - +
321A GLY* 1.3 74.3 - - - +
323A HIS* 1.3 70.3 + - - +
325A ALA* 3.1 2.8 + - - +
326A ILE* 2.7 34.1 + - + +
392A ILE* 5.6 2.2 - - + -
472A ILE* 3.9 26.5 - - + -
483A B7G 6.1 0.2 - - + -
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Residues in contact with HIS 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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289A THR* 4.1 5.8 - - + +
293A VAL* 5.5 0.4 - - + -
319A LYS 5.2 0.6 + - - -
320A TYR 5.3 1.6 + - - +
321A GLY 3.4 0.4 - - - -
322A VAL* 1.3 87.2 - - + +
324A GLU* 1.3 59.0 + - - +
326A ILE* 3.5 11.1 - - + +
327A PHE* 2.9 50.4 + + + -
446A VAL* 3.8 23.8 - - + -
449A HIS* 4.4 0.2 - + - -
469A LEU* 4.7 3.6 - - + -
472A ILE* 3.7 34.5 - - + +
473A TYR* 2.9 31.2 + + - -
482A 331 2.8 37.0 + + - -
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Residues in contact with GLU 324 (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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320A TYR 4.0 6.4 + - - +
321A GLY 3.2 8.6 + - - +
322A VAL 3.2 0.4 - - - -
323A HIS* 1.3 79.7 - - - +
325A ALA* 1.3 61.5 + - - +
328A ALA* 3.0 22.9 + - - +
391A ILE* 3.6 14.7 - - + +
397A ARG* 2.9 42.6 + - - -
439A MET 4.8 3.5 - - - +
442A LEU* 3.5 32.1 - - + +
443A ARG* 3.6 29.9 + - - +
446A VAL* 3.5 25.6 - - + +
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Residues in contact with ALA 325 (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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296A LEU* 3.9 25.4 - - + -
321A GLY 3.0 12.8 + - - +
322A VAL* 3.5 7.4 - - - +
324A GLU* 1.3 78.5 - - - +
326A ILE* 1.3 56.9 + - - +
328A ALA* 3.2 2.8 + - - +
329A MET* 3.0 36.0 + - - +
388A ILE* 4.1 15.9 - - + -
391A ILE* 4.0 13.6 - - + +
392A ILE* 4.2 9.2 - - + -
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Residues in contact with ILE 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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289A THR* 3.7 33.0 - - + +
292A THR* 3.9 12.6 - - + -
293A VAL* 3.9 18.4 - - + -
296A LEU* 3.6 15.3 - - + -
322A VAL* 2.7 32.9 + - + +
323A HIS* 3.5 13.2 - - + +
325A ALA* 1.3 73.4 - - - +
327A PHE* 1.3 69.9 + - + +
329A MET* 3.4 2.5 + - - -
330A LEU 2.8 23.0 + - - -
482A 331 2.9 44.0 - - + -
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Residues in contact with PHE 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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323A HIS* 2.9 28.7 + + + +
326A ILE* 1.3 82.3 - - + +
328A ALA* 1.3 66.8 + - - +
330A LEU* 3.6 22.2 - - + +
331A ALA 3.9 2.6 + - - -
367A LYS* 3.4 42.6 - - + -
370A PHE* 4.1 12.5 - - - -
371A ALA* 5.7 0.3 - - - +
442A LEU* 3.8 15.7 - - + -
445A LEU* 4.0 14.8 - - + -
446A VAL* 4.0 18.8 - - + -
449A HIS* 3.8 36.6 - + + -
482A 331 3.5 31.2 - + + -
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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 GLU 3.0 13.8 + - - +
325A ALA* 3.3 10.1 - - - +
326A ILE 3.1 0.2 - - - -
327A PHE* 1.3 78.3 - - - +
329A MET* 1.3 64.7 + - + +
331A ALA* 3.2 23.2 + - - +
332A SER* 4.3 1.2 + - - -
370A PHE* 4.6 4.5 - - - -
374A PHE* 3.9 12.2 - - + -
384A LEU* 5.4 3.3 - - + +
387A PHE* 4.0 30.1 - - + -
388A ILE* 5.3 3.1 - - + -
391A ILE* 4.1 5.2 - - + -
442A LEU* 3.8 10.7 - - + +
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Residues in contact with MET 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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222A TYR* 4.2 8.1 - - + +
226A PHE* 3.4 42.8 - - + -
228A MET 5.6 3.6 - - - +
292A THR* 4.5 8.3 - - - -
296A LEU* 4.0 17.7 - - - -
325A ALA 3.0 17.8 + - - +
326A ILE* 3.9 1.8 - - - +
328A ALA* 1.3 69.7 - - - +
330A LEU* 1.3 65.3 + - - +
331A ALA 3.0 2.7 - - - -
332A SER* 2.9 28.6 + - - +
333A ILE* 3.9 2.6 + - - +
384A LEU* 5.7 5.8 - - + -
388A ILE* 3.3 35.9 - - + -
482A 331 3.3 27.3 - - - -
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Residues in contact with LEU 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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326A ILE 2.8 10.4 + - - +
327A PHE* 3.6 15.7 - - + +
328A ALA 3.2 0.4 - - - -
329A MET* 1.3 76.6 - - - +
331A ALA* 1.3 64.4 + - - +
333A ILE* 3.1 27.6 + - + +
334A VAL* 3.4 21.8 - - + +
339A LEU* 4.8 7.4 - - + -
364A ILE* 5.5 2.9 - - + -
367A LYS* 3.6 37.9 - - + +
368A PHE* 5.4 0.7 - - + +
371A ALA* 5.5 0.7 - - + -
482A 331 3.4 65.5 - - + +
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Residues in contact with ALA 331 (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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234A ARG* 3.5 0.3 + - - -
327A PHE 3.9 3.4 + - - +
328A ALA 3.2 15.3 + - - +
330A LEU* 1.3 79.0 - - - +
332A SER* 1.3 63.0 + - - +
334A VAL* 3.2 8.4 + - - +
370A PHE* 5.3 0.7 - - + -
371A ALA* 3.6 29.8 - - + +
374A PHE* 3.6 19.5 - - + -
375A ASN* 2.9 38.3 + - - +
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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