Contacts of the helix formed by residues 343 - 365 (chain C) in PDB entry 1Y9D
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 THR 343 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C GLU 5.5 0.8 + - - -
238C LYS* 4.4 11.6 + - + +
340C ARG* 5.1 16.6 - - + +
341C GLU 3.6 15.3 - - - +
342C SER* 1.3 72.8 + - - +
344C PRO* 1.3 75.0 - - - +
345C TRP* 3.8 7.6 + - - +
346C TRP* 3.2 24.3 + - - +
347C GLN* 3.2 25.1 + - - +
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Residues in contact with PRO 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C THR* 1.3 87.1 - - - +
345C TRP* 1.3 60.5 + - + +
347C GLN* 3.1 2.7 + - + -
348C ALA* 2.9 32.1 + - - +
589C PHE* 3.3 36.6 - - + +
591C LEU* 3.8 23.3 - - + -
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Residues in contact with TRP 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C GLU 3.7 14.4 - - - +
214C ARG* 3.5 40.5 - - + -
215C PRO* 2.9 39.4 + - + -
216C LEU* 3.8 22.2 - - + -
238C LYS 5.0 2.9 - - - -
240C PRO* 3.6 17.1 - - + +
273C ALA* 3.6 25.8 - - - -
276C GLN* 3.7 23.3 - - + -
343C THR* 4.0 7.2 - - - +
344C PRO* 1.3 80.1 - - + +
346C TRP* 1.3 62.0 + - - +
348C ALA* 3.9 1.4 - - - +
349C ASN* 3.0 52.5 + - - -
582C LEU* 5.0 2.9 - - + -
586C LEU* 4.5 12.6 - - + -
591C LEU* 3.6 24.1 - - + +
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Residues in contact with TRP 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C SER 3.4 20.0 - - - -
235C LYS* 4.8 5.8 - - + -
238C LYS* 3.2 52.8 - - + +
239C ILE 3.5 14.8 - - - -
240C PRO* 4.1 6.1 - - + -
255C TYR* 3.4 24.2 - + - -
257C ALA* 3.5 26.7 - - + -
342C SER* 3.2 22.9 - - - -
343C THR* 3.2 23.5 + - - +
345C TRP* 1.3 82.2 - - - +
347C GLN* 1.3 59.2 + - - +
349C ASN* 3.6 3.5 + - - +
350C LEU* 3.0 63.5 + - + +
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Residues in contact with GLN 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C SER* 2.7 35.2 + - - +
343C THR 3.2 8.2 + - - +
344C PRO* 3.1 3.4 + - + +
346C TRP* 1.3 87.7 - - - +
348C ALA* 1.3 60.3 + - - +
350C LEU* 3.8 17.7 - - - +
351C ALA* 3.0 28.8 + - - +
589C PHE* 3.6 37.3 - - + -
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Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C PRO 2.9 17.9 + - - +
345C TRP* 3.9 4.5 - - - +
347C GLN* 1.3 75.0 - - - +
349C ASN* 1.3 59.3 + - - +
351C ALA 3.3 1.0 + - - -
352C ASN* 2.9 24.9 + - - +
582C LEU* 4.3 3.5 - - + +
585C TYR* 3.4 40.2 - - + +
586C LEU* 4.2 19.3 - - + +
589C PHE* 3.8 11.7 - - + -
591C LEU* 4.7 0.7 - - + -
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Residues in contact with ASN 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PRO* 3.6 21.4 - - + +
257C ALA* 6.2 1.8 - - + -
259C LEU* 4.1 15.0 - - + +
269C PRO 4.9 1.4 - - - +
273C ALA* 3.7 20.9 - - - +
345C TRP* 3.0 58.9 + - - +
346C TRP 4.0 2.9 - - - +
348C ALA* 1.3 76.7 - - - +
350C LEU* 1.3 59.8 + - - +
351C ALA 3.1 0.2 - - - -
352C ASN* 3.2 7.8 + - - +
353C VAL* 2.8 36.1 + - - +
582C LEU* 4.3 13.3 - - - +
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C PRO* 3.6 41.2 - - + +
257C ALA* 4.1 13.2 - - + +
346C TRP* 3.0 62.3 + - + +
347C GLN* 3.8 23.6 - - - +
348C ALA 3.4 0.2 - - - -
349C ASN* 1.3 75.5 - - - +
351C ALA* 1.3 56.8 + - - +
353C VAL* 3.5 1.9 + - - +
354C LYS* 3.0 28.9 + - - +
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C GLN 3.0 19.5 + - - +
348C ALA 3.5 2.9 - - - +
349C ASN 3.1 0.2 - - - -
350C LEU* 1.3 75.0 - - - +
352C ASN* 1.3 60.7 + - - +
354C LYS* 3.5 8.1 + - - +
355C ASN* 2.9 28.6 + - - +
585C TYR* 3.4 33.5 + - + -
588C GLN* 4.8 2.9 - - - +
589C PHE* 4.3 9.2 - - + -
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Residues in contact with ASN 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 6.3 0.2 - - + -
268C LYS* 2.8 23.3 + - - -
269C PRO* 3.9 20.0 + - + +
272C GLU* 2.8 25.5 + - - +
348C ALA 2.9 14.4 + - - +
349C ASN* 3.5 11.7 + - - +
351C ALA* 1.3 73.7 - - - +
353C VAL* 1.3 68.5 + - - +
355C ASN* 3.1 3.6 + - - +
356C TRP* 2.9 24.8 + - - +
580C GLN 3.9 1.6 - - - +
582C LEU* 3.4 27.4 - - + +
585C TYR* 3.6 18.5 - - + -
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Residues in contact with VAL 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C PRO* 3.3 25.8 - - + +
257C ALA* 5.0 0.2 - - - -
258C TYR 3.8 9.9 - - - +
259C LEU* 3.5 28.7 - - + -
269C PRO* 4.1 17.0 - - + -
349C ASN 2.8 23.7 + - - +
350C LEU 3.8 1.8 - - - +
352C ASN* 1.3 73.2 - - - +
354C LYS* 1.3 55.0 + - - +
356C TRP* 3.3 2.3 + - + +
357C ARG* 2.8 71.8 + - + +
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Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C LEU 3.0 18.1 + - - +
351C ALA* 3.6 8.5 - - - +
353C VAL* 1.3 74.4 - - - +
355C ASN* 1.3 69.4 + - - +
357C ARG* 3.6 6.4 + - - +
358C ALA* 3.2 22.7 + - + +
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Residues in contact with ASN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C LYS* 4.0 1.2 + - - -
351C ALA 2.9 12.4 + - - +
352C ASN* 3.4 8.1 - - - +
354C LYS* 1.3 73.4 - - - +
356C TRP* 1.3 54.3 + - - +
358C ALA* 2.8 29.2 + - - +
359C TYR* 2.9 11.5 + - - +
578C ASP* 2.8 25.8 + - - +
579C LEU* 3.4 12.1 - - - +
580C GLN* 2.7 34.4 + - - +
585C TYR* 3.1 29.7 + - + +
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Residues in contact with TRP 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C LEU 5.4 0.4 - - - -
267C GLN* 2.7 28.6 - - - +
268C LYS* 3.7 47.5 - - + +
269C PRO* 3.4 30.7 - - + +
352C ASN 2.9 14.6 + - - +
353C VAL* 3.5 8.3 - - + +
355C ASN* 1.3 71.3 + - - +
357C ARG* 1.3 67.3 + - + +
359C TYR* 3.1 29.4 + + - +
360C LEU* 3.0 43.2 + - + +
403C ARG* 3.7 40.2 - - + -
550C LEU* 3.8 26.0 - - + -
579C LEU* 4.0 10.3 - - + +
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Residues in contact with ARG 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ASP 2.8 19.6 + - - -
254C ARG* 2.7 31.1 + - - +
255C TYR 2.7 22.1 + - - -
256C PRO* 4.0 4.0 - - - +
258C TYR* 3.1 26.3 + - - +
353C VAL* 2.8 40.6 + - + +
354C LYS* 4.1 6.5 - - - +
356C TRP* 1.3 80.5 - - + +
358C ALA* 1.3 56.4 + - - +
360C LEU* 3.8 12.0 - - + +
361C ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C LYS* 3.2 13.6 + - + +
355C ASN* 2.8 12.7 + - - +
357C ARG* 1.3 75.1 - - - +
359C TYR* 1.3 61.1 + - - +
361C ALA* 3.8 6.3 - - - +
362C SER* 2.9 29.5 + - - -
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Residues in contact with TYR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ASN* 2.9 6.7 + - - +
356C TRP* 3.3 40.8 - + - +
358C ALA* 1.3 75.9 - - - +
360C LEU* 1.3 70.3 + - + +
362C SER* 2.8 26.5 + - - -
363C LEU* 3.3 34.0 + - + +
374C TYR* 5.3 2.4 + - - -
403C ARG* 5.7 0.4 - - - -
550C LEU* 3.7 25.7 + - + +
574C TYR* 2.6 34.3 + - - +
575C GLU 3.4 17.0 - - - -
576C ALA* 3.8 9.4 - - + -
578C ASP* 6.0 1.1 - - - -
579C LEU* 3.6 30.5 - - + +
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Residues in contact with LEU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C GLN* 4.3 2.2 - - - +
356C TRP* 3.0 57.9 + - + +
357C ARG* 3.9 11.4 - - + +
359C TYR* 1.3 90.4 - - + +
361C ALA* 1.3 65.7 + - - +
363C LEU* 3.2 10.3 + - + +
364C GLU* 3.1 34.0 + - - +
403C ARG* 3.8 32.8 - - + +
404C HIS* 4.0 24.7 - - + +
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Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C ARG 3.0 19.1 + - - +
358C ALA* 3.4 7.6 + - - +
359C TYR 3.3 0.2 - - - -
360C LEU* 1.3 75.9 - - - +
362C SER* 1.3 57.4 + - - +
364C GLU* 3.3 11.8 + - - +
365C ASP* 2.9 47.4 + - - +
406C LYS* 6.3 1.1 - - - +
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Residues in contact with SER 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ALA 2.9 18.2 + - - -
359C TYR* 2.8 19.9 + - - -
360C LEU 3.1 0.6 - - - -
361C ALA* 1.3 79.1 - - - +
363C LEU* 1.3 65.9 + - - +
365C ASP* 3.8 9.0 + - - +
366C LYS* 3.8 15.4 + - - +
575C GLU* 4.9 4.2 + - - +
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C TYR* 3.6 42.6 - - + +
360C LEU* 3.2 16.4 + - + +
362C SER* 1.3 86.1 + - - +
364C GLU* 1.3 63.7 + - - +
365C ASP 3.3 0.7 + - - -
366C LYS* 3.6 11.2 + - - +
374C TYR* 3.7 51.4 - - + +
375C GLN* 3.1 22.3 + - - -
404C HIS* 4.6 0.7 - - + -
574C TYR 4.7 4.0 - - - +
575C GLU* 4.0 35.9 - - + +
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Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 3.1 22.2 + - - +
361C ALA* 3.8 11.2 - - - +
363C LEU* 1.3 76.1 - - - +
365C ASP* 1.3 61.2 + - - +
366C LYS 3.4 0.2 - - - -
374C TYR* 3.9 17.2 - - - +
375C GLN* 3.8 2.0 - - - +
378C ARG* 2.8 61.0 + - + +
381C ASN* 4.3 9.4 + - - -
403C ARG 5.0 0.5 - - - +
404C HIS* 3.0 42.4 + - + +
406C LYS* 4.1 20.1 + - - -
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Residues in contact with ASP 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ALA* 2.9 32.2 + - - +
362C SER* 3.8 4.9 + - - +
363C LEU 3.2 0.4 - - - -
364C GLU* 1.3 85.1 - - - +
366C LYS* 1.3 70.3 + - - +
367C GLN* 3.4 18.0 + - - +
378C ARG* 4.8 7.5 + - - +
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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