Contacts of the helix formed by residues 335 - 358 (chain C) in PDB entry 5Y1Z
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 335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.3 34.3 - - + +
14A LEU* 5.7 2.9 - - + -
15A ALA* 5.7 6.3 - - + +
18A GLU* 3.7 21.1 - - - +
288C PHE* 5.1 2.5 - - + -
289C PRO* 4.9 5.3 - - + +
291C TRP* 4.1 10.7 - - - -
334C LYS* 1.4 85.0 - - + +
336C LYS* 1.3 65.1 + - - +
337C SER 3.2 3.0 + - - -
338C ILE* 3.3 33.5 - - + +
339C PHE* 3.5 7.9 + - - +
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Residues in contact with LYS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 4.0 1.8 + - - -
334C LYS* 3.8 6.3 - - - +
335C THR* 1.3 74.4 - - - +
337C SER* 1.3 64.8 + - - +
339C PHE* 3.1 10.8 + - - +
340C ASN* 2.9 33.7 + - - +
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.0 23.5 + - - +
21A ILE* 5.8 3.8 - - - +
336C LYS* 1.3 77.7 - - - +
338C ILE* 1.3 64.8 + - - +
340C ASN* 3.1 12.1 + - - +
341C SER* 3.0 23.8 + - - -
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Residues in contact with ILE 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.6 44.4 - - + +
17A TYR* 3.8 31.6 - - + +
18A GLU* 3.7 13.7 + - + +
21A ILE* 6.2 0.4 - - + -
288C PHE* 5.1 0.2 - - + -
291C TRP* 3.8 12.0 - - + -
309C GLY* 5.6 0.3 - - - -
310C GLN* 4.6 11.6 + - - +
335C THR* 3.3 29.8 - - - +
337C SER* 1.3 76.8 - - - +
339C PHE* 1.3 60.2 + - - +
341C SER* 3.2 9.7 + - - -
342C ALA* 2.9 28.8 + - - +
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Residues in contact with PHE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C TRP* 4.0 9.9 - + - -
289C PRO* 5.9 2.2 - - + -
290C PHE 3.7 19.3 - - - -
291C TRP* 3.5 32.8 - + + -
292C PRO* 4.3 1.8 - - + -
328C ILE* 4.3 27.4 - - + -
335C THR 3.7 9.9 - - - +
336C LYS* 3.1 13.2 + - - +
338C ILE* 1.3 82.5 - - - +
340C ASN* 1.3 69.6 + - - +
342C ALA* 3.1 3.8 + - - +
343C MET* 2.8 69.6 + - + +
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Residues in contact with ASN 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C LYS* 2.9 25.7 + - - +
337C SER* 3.1 10.1 + - - +
339C PHE* 1.3 87.3 - - - +
341C SER* 1.3 62.5 + - - +
343C MET* 3.4 7.9 + - - +
344C GLN* 3.0 35.5 + - - +
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Residues in contact with SER 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLY* 5.5 2.0 - - - -
337C SER* 3.0 13.6 + - - -
338C ILE* 3.4 13.2 - - - -
339C PHE 3.2 0.2 - - - -
340C ASN* 1.3 75.4 - - - +
342C ALA* 1.3 63.7 + - - +
344C GLN* 3.1 14.4 + - - +
345C GLU* 3.0 21.3 + - - +
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Residues in contact with ALA 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C TRP* 3.6 31.4 - - + +
292C PRO* 4.0 8.3 - - + -
308C PHE* 3.8 5.8 - - - +
309C GLY* 3.8 24.8 - - - +
338C ILE 2.9 16.3 + - - +
339C PHE 3.5 7.2 - - - +
341C SER* 1.3 73.4 - - - +
343C MET* 1.3 57.5 + - - +
345C GLU* 3.1 4.9 + - - +
346C MET* 2.8 29.3 + - - +
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Residues in contact with MET 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C TRP* 3.3 32.3 - - + -
292C PRO* 3.3 41.1 - - + -
324C MET* 5.3 0.2 - - - +
339C PHE* 2.8 47.4 + - + +
340C ASN* 3.6 9.9 - - - +
342C ALA* 1.3 72.7 - - - +
344C GLN* 1.3 63.8 + - + +
346C MET* 3.1 22.5 + - - +
347C GLU* 2.8 37.4 + - - +
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Residues in contact with GLN 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ASN* 3.0 25.9 + - - +
341C SER* 3.4 12.5 + - - +
343C MET* 1.3 75.6 - - + +
345C GLU* 1.3 63.1 + - - +
347C GLU* 3.1 17.1 + - - +
348C VAL* 3.0 29.2 + - + +
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Residues in contact with GLU 345 (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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110A GLN* 4.8 2.9 - - - +
268C ASN* 5.6 2.6 - - - +
270C PHE* 4.2 5.6 - - - +
271C CYS* 3.6 23.8 - - - -
308C PHE* 3.4 15.1 - - + -
309C GLY* 2.8 31.3 + - - -
311C HIS* 2.7 32.4 + - - -
341C SER 3.0 12.2 + - - +
342C ALA* 3.1 8.3 + - - +
344C GLN* 1.3 76.2 - - - +
346C MET* 1.3 62.6 + - - +
348C VAL* 3.3 10.1 + - - +
349C TYR* 3.0 18.5 + - - +
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Residues in contact with MET 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 3.6 19.3 - - + -
292C PRO* 3.8 10.1 - - + -
308C PHE* 3.5 29.9 - - + -
324C MET* 3.5 48.5 - - + +
342C ALA 2.8 12.5 + - - +
343C MET* 3.1 19.0 + - - +
345C GLU* 1.3 76.5 - - - +
347C GLU* 1.3 66.3 + - + +
349C TYR* 3.0 5.7 + - - +
350C VAL* 2.8 30.3 + - + +
362C TYR* 3.8 23.8 - - + +
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Residues in contact with GLU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C MET* 2.8 27.8 + - - +
344C GLN* 3.1 19.5 + - - +
346C MET* 1.3 79.9 - - + +
348C VAL* 1.3 66.3 + - - +
350C VAL* 3.2 8.4 + - - +
351C GLU* 3.0 22.2 + - - +
362C TYR* 4.4 15.2 + - - +
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ASN* 4.8 14.4 - - + +
271C CYS* 3.9 20.4 - - + -
344C GLN* 3.0 17.6 + - + +
345C GLU* 3.5 9.4 - - - +
347C GLU* 1.3 73.9 - - + +
349C TYR* 1.3 65.9 + - - +
351C GLU* 3.1 9.9 + - + +
352C ASN* 2.9 30.6 + - - +
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Residues in contact with TYR 349 (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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270C PHE 4.0 4.0 - - - -
271C CYS* 3.3 37.4 - - - +
272C GLU 4.0 2.7 - - - -
273C PRO* 3.8 24.5 - - + +
274C CYS 4.8 1.1 + - - -
277C PRO* 4.0 7.6 - - - +
278C HIS* 3.7 20.7 + + - +
280C LEU* 3.5 39.3 - - + -
294C LYS* 3.8 21.0 - - - +
308C PHE* 3.9 11.2 - + + -
345C GLU 3.0 13.3 + - - +
346C MET 3.0 9.4 + - - +
348C VAL* 1.3 77.6 - - - +
350C VAL* 1.3 58.7 + - - +
352C ASN* 3.1 3.6 + - - +
353C ILE* 2.8 51.6 + - + +
360C PHE* 5.4 2.2 - + - -
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Residues in contact with VAL 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 4.1 14.8 - - + -
346C MET* 2.8 25.5 + - + +
347C GLU* 3.5 9.9 - - + +
348C VAL 3.2 0.4 - - - -
349C TYR* 1.3 72.5 - - - +
351C GLU* 1.3 64.5 + - - +
353C ILE* 3.0 10.9 - - - +
354C ARG* 2.9 57.9 + - - +
360C PHE* 3.9 28.7 - - + -
362C TYR* 3.8 21.3 - - - +
504C SO4 5.0 0.7 - - - +
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Residues in contact with GLU 351 (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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347C GLU 3.0 13.9 + - - +
348C VAL* 3.5 10.3 - - + +
350C VAL* 1.3 77.7 - - - +
352C ASN* 1.3 64.5 + - - +
354C ARG* 3.1 9.8 + - - +
355C ARG* 2.9 64.1 + - - +
96D ARG* 3.0 42.9 + - - +
97D GLU 4.8 1.2 - - - +
506D GOL 5.8 1.8 - - - -
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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
----------------------------------------------------------
268C ASN* 5.9 0.8 - - - +
271C CYS* 3.1 29.9 + - - +
272C GLU* 4.1 14.5 + - - -
273C PRO* 3.7 19.9 - - + +
348C VAL* 2.9 23.8 + - - +
349C TYR 3.1 6.9 + - - +
351C GLU* 1.3 78.9 - - - +
353C ILE* 1.3 57.2 + - - +
355C ARG* 3.2 19.9 + - - +
356C LYS* 2.9 30.1 + - - +
113D LYS* 5.9 3.1 - - - +
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Residues in contact with ILE 353 (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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273C PRO* 3.4 29.8 - - + +
277C PRO* 3.4 28.3 - - + -
349C TYR* 2.8 24.2 + - + +
350C VAL* 3.0 24.9 + - - +
352C ASN* 1.3 75.2 - - - +
354C ARG* 1.3 58.2 + - - +
356C LYS* 4.4 1.3 - - - +
357C PHE* 2.8 41.0 + - + +
358C GLY 3.6 2.3 + - - -
359C VAL 3.8 1.9 - - - +
360C PHE* 3.5 32.5 - - + -
377C MET* 3.8 18.8 - - + -
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Residues in contact with ARG 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 VAL* 2.9 31.3 + - - +
351C GLU* 3.1 13.1 + - - +
353C ILE* 1.3 77.4 - - - +
355C ARG* 1.3 58.3 + - - +
358C GLY* 3.0 30.5 + - - +
359C VAL* 3.9 6.7 - - - +
360C PHE* 2.8 45.3 + - + +
362C TYR* 3.8 20.2 - - - -
504C SO4 3.2 28.9 + - - -
505C SO4 3.2 30.8 + - - +
94D CYS 5.2 1.4 - - - +
96D ARG* 3.6 42.9 - - - +
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Residues in contact with ARG 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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351C GLU* 2.9 50.6 + - - +
352C ASN* 3.8 15.8 + - - +
354C ARG* 1.3 77.8 - - - +
356C LYS* 1.3 64.1 + - - +
358C GLY 4.8 0.5 + - - -
93D VAL* 6.0 0.2 - - - +
94D CYS* 3.5 32.3 - - + +
96D ARG* 4.0 8.5 - - - +
97D GLU 3.8 3.4 + - - -
111D HIS* 3.1 50.1 + - - +
113D LYS* 5.5 7.5 - - - +
114D CYS* 4.6 8.9 - - - -
502D ZN 4.4 1.1 - - - -
506D GOL 3.1 42.0 + - - -
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Residues in contact with LYS 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PRO* 4.6 9.4 - - + -
352C ASN 2.9 16.3 + - - +
353C ILE* 4.0 3.1 - - - +
355C ARG* 1.3 79.8 - - - +
357C PHE* 1.3 80.8 + - + +
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Residues in contact with PHE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PRO* 4.3 2.9 - - + -
274C CYS 3.7 11.2 - - - -
275C SER* 3.4 29.4 - - - -
277C PRO* 3.7 17.0 - - + -
353C ILE* 2.8 44.4 + - + +
356C LYS* 1.3 90.4 - - + +
358C GLY* 1.3 61.2 + - - +
359C VAL* 3.4 3.0 - - - +
377C MET* 4.3 12.3 - - - -
379C LEU* 5.6 1.4 - - - +
389C ALA* 3.4 37.7 - - + +
390C LYS 4.6 19.7 - - - -
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Residues in contact with GLY 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ILE 3.6 0.8 + - - -
354C ARG* 3.0 26.3 + - - +
355C ARG 4.6 0.4 - - - -
356C LYS 3.8 0.4 - - - -
357C PHE* 1.3 76.4 - - - +
359C VAL* 1.3 68.2 + - - +
96D ARG* 5.2 4.3 + - - -
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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