Contacts of the helix formed by residues 362 - 386 (chain A) in PDB entry 1YTS
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A SER* 1.3 70.9 - - - +
363A GLU* 1.3 58.5 + - - +
365A THR* 3.1 7.1 + - - -
366A LYS* 2.8 44.9 + - - +
453A VAL* 4.1 15.3 + - - +
456A LYS* 4.0 30.7 + - - +
457A LEU* 4.1 17.9 - - - +
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Residues in contact with GLU 363 (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 LEU 4.5 2.6 - - - +
325A ASP* 5.4 2.7 - - - +
361A SER* 3.2 8.4 + - - +
362A SER* 1.3 75.1 - - - +
364A VAL* 1.3 67.8 + - + +
366A LYS* 2.9 40.7 + - - +
367A ALA* 3.2 22.5 + - - +
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.1 21.5 - - + +
324A GLY* 3.7 23.8 - - - +
325A ASP* 4.0 14.1 - - + +
327A ILE* 3.6 33.9 - - + -
360A VAL* 4.0 16.8 - - + -
361A SER* 3.1 25.0 + - - +
363A GLU* 1.3 75.5 - - + +
365A THR* 1.3 57.8 + - - +
367A ALA* 3.3 2.1 + - - +
368A LEU* 2.8 33.8 + - + +
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TRP* 5.7 2.0 - - + -
360A VAL* 3.7 7.4 + - + +
361A SER 2.6 21.7 + - - -
362A SER 3.4 7.2 - - - -
364A VAL* 1.3 77.6 - - - +
366A LYS* 1.3 52.6 + - - +
368A LEU* 3.2 8.3 + - + +
369A ALA* 2.8 36.4 + - - +
412A GLN* 3.5 38.3 + - + +
413A LEU* 4.8 5.6 - - + +
416A ALA* 3.4 27.8 - - + -
453A VAL* 3.6 5.4 - - + +
457A LEU* 4.1 9.6 - - + -
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Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 2.8 32.1 + - - +
363A GLU* 2.9 40.6 + - - +
365A THR* 1.3 70.4 - - - +
367A ALA* 1.3 65.1 + - - +
369A ALA* 3.2 5.4 + - - +
370A SER* 3.0 27.9 + - - -
416A ALA* 5.7 1.1 - - - -
420A ASN* 5.3 2.5 + - - +
456A LYS 6.0 0.2 + - - -
457A LEU* 3.6 26.0 - - + +
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.8 30.2 - - + +
363A GLU* 3.2 17.0 + - - +
364A VAL 3.5 3.4 - - - +
366A LYS* 1.3 80.2 - - - +
368A LEU* 1.3 57.2 + - - +
370A SER* 3.7 6.5 + - - -
371A LEU* 3.1 26.9 + - - +
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Residues in contact with LEU 368 (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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285A LEU* 4.3 2.0 - - + -
323A LEU* 4.0 19.5 - - + +
327A ILE* 6.4 0.2 - - + -
349A VAL* 4.4 8.5 - - + -
351A VAL* 3.7 33.2 - - + -
354A TRP* 4.0 28.3 - - + -
360A VAL* 5.3 2.7 - - + -
364A VAL* 2.8 19.2 + - + +
365A THR* 3.5 7.9 - - + +
367A ALA* 1.3 74.5 - - - +
369A ALA* 1.3 68.6 + - - +
371A LEU* 3.0 5.2 + - + +
372A VAL* 2.8 37.1 + - + +
413A LEU* 3.8 24.7 - - + -
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR 2.8 20.0 + - - +
366A LYS* 3.5 6.1 - - - +
368A LEU* 1.3 73.3 - - - +
370A SER* 1.3 62.8 + - - +
372A VAL* 3.2 2.1 + - - +
373A ASP* 2.8 26.3 + - - +
413A LEU* 3.8 20.6 - - + +
416A ALA* 4.1 23.3 - - + +
417A MET* 4.3 6.0 - - + +
420A ASN* 4.1 17.7 - - - +
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Residues in contact with SER 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LYS 3.0 18.3 + - - -
367A ALA* 3.8 6.5 - - - -
369A ALA* 1.3 74.4 - - - +
371A LEU* 1.3 59.7 + - - +
373A ASP* 3.7 3.0 - - - +
374A GLN* 2.9 45.0 + - - +
420A ASN* 4.1 14.9 + - - +
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Residues in contact with LEU 371 (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 GLN* 5.6 0.9 - - - +
321A VAL* 4.3 17.3 - - + -
323A LEU* 4.0 18.6 - - + -
329A ALA* 3.9 16.8 - - + -
331A MET* 3.6 34.5 - - + -
349A VAL* 4.1 12.3 - - + -
367A ALA 3.1 14.1 + - - +
368A LEU* 3.0 6.5 + - + +
370A SER* 1.3 78.4 - - - +
372A VAL* 1.3 56.8 + - - +
374A GLN* 4.0 12.1 - - + +
375A THR* 2.5 43.5 + - - +
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Residues in contact with VAL 372 (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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281A VAL* 3.8 18.7 - - + +
283A ALA* 4.0 27.8 - - + -
349A VAL* 4.1 23.6 - - + -
368A LEU* 2.8 27.0 + - + +
369A ALA* 3.8 4.5 - - - +
371A LEU* 1.3 73.4 - - - +
373A ASP* 1.4 63.5 + - - +
375A THR* 3.4 6.6 + - - -
376A ALA* 3.0 22.5 + - - +
399A PRO* 5.3 0.2 - - + -
401A ILE* 5.4 0.9 - - + -
413A LEU* 4.5 4.9 - - + -
417A MET* 3.6 32.1 - - + -
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Residues in contact with ASP 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 5.9 1.6 - - - +
369A ALA 2.8 19.0 + - - +
370A SER* 3.8 4.3 - - - +
372A VAL* 1.4 69.8 - - - +
374A GLN* 1.3 64.2 + - - +
376A ALA* 3.1 8.5 + - - +
377A GLU* 2.9 26.3 + - - +
380A ARG* 5.6 3.6 + - - -
399A PRO* 5.9 0.3 - - - +
417A MET* 3.9 30.5 - - - +
420A ASN* 2.9 35.4 + - - +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A SER* 2.9 31.4 + - - +
371A LEU* 4.0 10.8 - - + +
373A ASP* 1.3 72.6 - - - +
375A THR* 1.3 63.0 + - - +
377A GLU* 3.2 9.2 + - + +
378A THR* 3.1 30.8 + - - +
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Residues in contact with THR 375 (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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280A PRO 3.7 0.6 - - - +
281A VAL* 3.6 24.9 - - + -
331A MET* 5.1 5.5 - - - -
347A PRO* 3.8 20.7 - - + +
349A VAL* 4.3 10.3 - - + +
371A LEU* 2.5 35.8 + - - +
372A VAL* 3.6 5.1 - - - -
374A GLN* 1.3 77.0 - - - +
376A ALA* 1.3 62.1 + - - +
378A THR* 3.6 5.5 + - - -
379A LYS* 3.2 23.4 + - - +
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Residues in contact with ALA 376 (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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280A PRO* 3.4 22.3 - - + +
281A VAL* 3.9 14.1 - - + +
372A VAL* 3.0 13.7 + - + +
373A ASP* 3.3 13.2 - - - +
375A THR* 1.3 74.7 - - - +
377A GLU* 1.3 54.0 - - - +
379A LYS 3.3 1.9 + - - -
380A ARG* 2.8 60.0 + - - +
399A PRO* 5.1 4.0 - - + -
417A MET* 6.3 0.4 - - + -
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Residues in contact with GLU 377 (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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373A ASP 2.9 13.7 + - - +
374A GLN* 3.3 13.0 - - + +
376A ALA* 1.3 73.0 - - - +
378A THR* 1.3 65.1 + - - +
379A LYS 3.2 1.3 - - - -
380A ARG* 4.0 18.6 + - + +
381A ASN* 2.9 27.0 + - + +
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Residues in contact with THR 378 (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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374A GLN* 3.1 18.1 + - - +
375A THR* 4.0 6.8 - - - -
377A GLU* 1.3 76.9 - - - +
379A LYS* 1.3 61.5 + - - +
381A ASN* 3.6 6.6 + - - +
382A MET* 3.2 20.1 + - - +
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Residues in contact with LYS 379 (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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279A THR 4.6 0.4 - - - +
280A PRO* 3.2 33.7 - - + +
345A SER* 3.4 36.9 + - - +
347A PRO* 3.6 20.0 - - + -
375A THR 3.2 5.8 + - - +
376A ALA 3.4 4.3 - - - +
377A GLU 3.2 0.6 - - - -
378A THR* 1.3 77.5 - - - +
380A ARG* 1.3 64.7 + - - +
382A MET* 3.1 47.2 + - + +
383A TYR* 3.3 28.9 + - + -
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Residues in contact with ARG 380 (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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255A ARG* 4.1 26.9 + - - +
280A PRO* 3.8 12.2 - - + +
373A ASP* 5.6 3.6 + - - -
376A ALA* 2.8 42.4 + - - +
377A GLU* 4.0 18.1 + - - +
379A LYS* 1.3 70.7 - - - +
381A ASN* 1.4 60.6 + - - +
383A TYR* 3.0 18.4 + - - +
384A GLU* 3.1 16.2 + - - +
391A VAL* 5.0 1.9 - - - +
397A LEU* 3.0 51.3 + - + +
399A PRO* 3.7 20.8 - - - +
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Residues in contact with ASN 381 (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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377A GLU* 2.9 24.1 + - + +
378A THR* 3.9 7.2 + - - +
380A ARG* 1.4 71.0 - - - +
382A MET* 1.3 57.1 + - - +
384A GLU* 3.6 17.4 + - - +
385A SER* 3.0 33.9 + - - -
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Residues in contact with MET 382 (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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378A THR 3.2 12.3 + - - +
379A LYS* 3.1 47.6 + - + +
381A ASN* 1.3 77.4 - - - +
383A TYR* 1.3 86.2 + - + +
385A SER* 3.0 19.0 + - - +
386A LYS* 3.0 43.2 - - - +
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Residues in contact with TYR 383 (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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2A SO4 4.6 6.3 - - - -
278A ARG* 3.4 36.2 - - + +
279A THR 5.3 0.2 - - - -
280A PRO* 5.6 1.1 - - + -
344A ILE* 3.3 37.7 - - + +
345A SER 4.5 2.1 + - - -
379A LYS* 3.3 39.9 + - + -
380A ARG* 3.0 9.4 + - - +
382A MET* 1.3 93.2 - - + +
384A GLU* 1.3 59.9 + - - +
386A LYS* 3.2 7.1 + - + +
387A GLY 3.1 8.0 + - - -
388A SER* 2.8 56.1 + - - -
391A VAL* 4.0 7.9 - - + -
397A LEU* 3.7 18.4 - - + -
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Residues in contact with GLU 384 (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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380A ARG* 3.1 17.2 + - - +
381A ASN* 3.6 16.6 - - - +
383A TYR* 1.3 74.0 - - - +
385A SER* 1.3 58.1 + - - +
386A LYS 2.8 9.9 + - - -
387A GLY* 3.1 12.2 + - - +
388A SER 4.9 0.2 - - - +
391A VAL* 4.0 26.7 - - + +
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASN* 3.0 22.3 + - - -
382A MET* 3.0 19.8 + - - +
384A GLU* 1.3 73.2 - - - +
386A LYS* 1.3 60.3 + - - +
387A GLY 3.5 0.2 - - - -
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A MET* 3.0 48.3 - - - +
383A TYR* 3.2 11.1 + - + +
384A GLU 2.8 1.2 + - - -
385A SER* 1.3 81.8 - - - +
387A GLY* 1.3 63.0 + - - +
388A SER* 4.6 1.6 - - - +
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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