Contacts of the helix formed by residues 332 - 355 (chain C) in PDB entry 4E2I
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 ASN 332 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN* 4.2 0.2 - - - +
270C TRP* 5.1 6.5 - - + -
330C SER* 3.2 10.3 + - - +
331C LYS* 1.3 94.5 - - - +
333C GLN* 1.3 64.7 + - - +
334C LYS 3.2 3.1 - - - +
335C THR* 3.6 28.4 + - + -
336C ILE* 3.0 29.7 + - + +
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Residues in contact with GLN 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B THR* 5.3 6.3 + - - +
339B GLN* 3.2 33.2 + - + +
343B THR* 3.7 21.6 + - - +
289C LEU* 3.2 26.8 - - + +
293C LEU* 3.8 24.2 - - - +
296C GLN* 4.9 0.2 - - - +
327C PHE* 3.3 38.0 - - + +
328C ALA* 3.0 28.9 - - - +
330C SER* 3.6 7.2 - - - +
332C ASN* 1.3 76.9 - - - +
334C LYS* 1.3 60.6 + - - +
337C CYS* 3.6 9.7 + - - -
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Residues in contact with LYS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLN* 5.3 3.0 + - - +
339B GLN* 4.8 6.2 - - + +
342B ASP* 4.0 34.4 + - + +
512B LYS* 4.8 11.5 - - - +
514B LEU* 5.5 5.3 - - - +
516B LYS* 4.6 17.8 - - - +
285C VAL* 4.1 23.0 - - + +
286C LEU* 4.6 7.9 - - + -
289C LEU* 4.6 17.9 - - + -
332C ASN 3.2 0.6 - - - -
333C GLN* 1.3 77.2 - - - +
335C THR* 1.3 61.6 + - - +
337C CYS* 4.0 3.1 - - - +
338C GLN* 3.0 33.9 + - + +
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Residues in contact with THR 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C TRP* 3.6 23.2 - - + -
332C ASN* 3.1 31.1 + - + +
334C LYS* 1.3 78.5 - - - +
336C ILE* 1.3 65.8 + - - +
338C GLN* 3.1 16.2 + - + +
339C GLN* 3.2 11.4 + - - +
331D LYS 5.5 1.8 - - - +
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Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C VAL* 3.9 20.6 - - + -
269C SER 4.6 0.7 - - - +
270C TRP* 3.6 46.0 - - + +
273C VAL* 3.6 33.8 - - + +
274C THR* 5.3 1.6 + - - -
327C PHE* 3.5 24.9 - - + -
330C SER* 3.3 25.6 - - - +
332C ASN* 3.0 14.3 + - + +
335C THR* 1.3 77.5 - - - +
337C CYS* 1.3 62.4 + - - +
339C GLN* 3.6 4.5 + - - +
340C ALA* 3.5 17.0 + - - +
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Residues in contact with CYS 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C VAL* 4.2 14.8 - - - -
285C VAL* 4.3 9.0 - - + +
288C LEU* 3.4 15.3 - - + +
289C LEU* 3.6 30.3 - - + -
292C TYR* 4.7 1.6 - - - -
327C PHE* 3.5 29.6 - - - -
333C GLN 3.6 9.5 + - - +
334C LYS* 4.3 3.4 - - - +
336C ILE* 1.3 77.2 - - - +
338C GLN* 1.3 64.7 + - - +
340C ALA* 3.3 10.2 + - - +
341C VAL* 3.0 27.8 + - - +
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Residues in contact with GLN 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU* 5.1 9.9 - - - +
285C VAL* 3.3 37.5 - - + +
334C LYS* 3.0 27.0 + - + +
335C THR* 3.1 13.2 + - + +
337C CYS* 1.3 77.9 - - - +
339C GLN* 1.3 63.8 + - - +
341C VAL* 3.1 20.0 + - - +
342C ASP* 3.0 38.6 + - - +
334D LYS* 5.0 5.9 + - - +
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Residues in contact with GLN 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C TRP* 3.2 30.5 - - + +
274C THR* 4.2 7.2 + - - +
335C THR 3.2 8.1 + - - +
336C ILE 3.9 7.2 - - - +
338C GLN* 1.3 78.1 - - - +
340C ALA* 1.3 62.4 + - - +
342C ASP* 3.2 13.6 + - + +
343C THR* 2.9 24.5 + - - +
289D LEU* 5.4 1.1 - - + +
330D SER 3.2 14.2 + - - +
331D LYS 3.5 10.5 + - - -
332D ASN* 4.0 0.2 - - - +
333D GLN* 2.9 65.5 + - + +
334D LYS* 4.5 6.0 - - + +
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C VAL* 4.1 4.9 - - + +
274C THR* 4.0 19.9 + - - +
277C ALA* 3.6 13.6 - - + +
288C LEU* 3.4 17.7 - - + -
336C ILE 3.5 10.8 + - - +
337C CYS* 3.3 11.4 + - - +
339C GLN* 1.3 79.4 - - - +
341C VAL* 1.3 64.0 + - - +
343C THR* 3.0 11.4 + - - -
344C VAL* 2.9 26.5 + - - +
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Residues in contact with VAL 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C CYS 4.3 0.7 - - - +
283C ASP* 3.4 30.3 - - - +
284C ASP 3.1 29.4 - - - +
285C VAL* 3.7 21.8 - - + -
288C LEU* 3.9 5.4 - - + -
337C CYS 3.0 17.5 - - - +
338C GLN* 3.1 10.1 + - - +
340C ALA* 1.3 77.3 - - - +
342C ASP* 1.3 56.8 + - - +
344C VAL* 3.0 11.6 + - - +
345C LEU* 2.9 39.1 + - + +
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Residues in contact with ASP 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C GLN* 3.0 36.0 + - - +
339C GLN* 3.2 13.2 + - + +
341C VAL* 1.3 78.1 - - - +
343C THR* 1.3 57.5 + - - +
345C LEU* 3.5 9.4 + - - +
346C ALA* 2.8 30.4 + - - +
516C LYS* 5.9 0.2 - - - -
286D LEU* 3.4 29.7 - - + +
289D LEU* 4.0 12.5 - - + +
334D LYS* 3.8 31.1 + - + +
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Residues in contact with THR 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C THR* 3.6 24.0 - - + +
278C MET* 3.5 31.4 - - + +
339C GLN* 2.9 14.4 + - - +
340C ALA 3.0 8.4 + - - -
342C ASP* 1.3 74.0 - - - +
344C VAL* 1.3 65.3 + - - +
346C ALA* 3.4 7.0 - - - +
347C LYS* 3.1 17.3 + - - +
289D LEU* 4.8 1.9 - - - +
293D LEU* 3.6 24.5 - - + +
333D GLN* 3.5 18.2 + - - +
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Residues in contact with VAL 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ALA* 3.7 28.5 - - + +
278C MET* 4.3 9.0 - - - +
281C LYS* 3.6 22.2 - - - +
282C CYS 3.2 23.6 - - - +
283C ASP* 3.9 4.7 - - + +
340C ALA 2.9 20.5 + - - +
341C VAL 3.0 6.7 + - - +
343C THR* 1.3 74.9 - - - +
345C LEU* 1.3 65.5 + - - +
347C LYS* 3.1 19.9 + - - +
348C LYS* 3.3 31.8 + - - +
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Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ASP* 3.9 30.5 - - + +
341C VAL* 2.9 30.9 + - + +
342C ASP* 4.0 9.9 - - - +
344C VAL* 1.3 77.3 - - - +
346C ALA* 1.3 52.5 + - - +
348C LYS* 3.4 14.9 + - + +
349C ARG* 2.8 37.3 + - - +
466C ASP* 4.9 1.0 - - - +
511C LYS* 4.3 25.1 - - + +
286D LEU* 4.3 24.9 - - + -
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Residues in contact with ALA 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C ASP 2.8 19.4 + - - +
343C THR* 3.4 11.9 - - - +
345C LEU* 1.3 76.3 - - - +
347C LYS* 1.3 65.3 + - - +
349C ARG* 3.1 9.3 + - - +
350C VAL* 3.0 29.7 + - - +
286D LEU* 3.5 22.9 - - - +
289D LEU* 4.6 4.7 - - + -
290D GLY* 3.5 19.3 - - - +
293D LEU* 4.9 0.7 - - + -
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Residues in contact with LYS 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C MET* 3.9 26.0 - - + +
343C THR 3.1 11.7 + - - +
344C VAL* 3.1 12.0 + - + +
346C ALA* 1.3 76.7 - - - +
348C LYS* 1.3 56.3 + - + +
350C VAL* 3.0 10.0 + - + +
351C ASP* 2.7 56.7 + - - +
290D GLY* 5.7 0.7 - - - -
294D GLU* 4.4 18.1 + - + +
304D LYS* 5.4 7.5 - - - +
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Residues in contact with LYS 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LYS* 3.7 23.2 + - - +
283C ASP* 4.4 11.9 - - - +
344C VAL* 3.3 34.9 + - - +
345C LEU* 3.8 17.0 - - + +
347C LYS* 1.3 79.1 - - + +
349C ARG* 1.3 62.7 + - - +
351C ASP* 4.0 9.1 - - - +
352C SER* 3.1 27.4 + - - -
466C ASP* 4.1 16.8 - - + +
467C GLN* 5.5 8.7 - - - +
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Residues in contact with ARG 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LEU* 2.8 15.7 + - - +
346C ALA* 3.1 17.7 + - - +
348C LYS* 1.3 77.1 - - - +
350C VAL* 1.3 56.2 + - - +
352C SER* 3.0 13.9 + - - -
353C LEU* 4.0 7.1 - - - +
465C ILE* 3.1 17.0 - - - +
466C ASP* 3.0 29.9 + - - -
511C LYS* 3.5 17.6 - - - +
516C LYS* 2.9 35.9 + - - +
517C ARG* 3.1 27.7 + - - +
284D ASP* 4.5 1.2 + - - -
286D LEU* 3.4 35.3 - - - +
287D LEU* 3.6 38.8 - - + +
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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
----------------------------------------------------------
346C ALA 3.0 16.1 + - - +
347C LYS* 3.0 10.5 + - + +
349C ARG* 1.3 76.7 - - - +
351C ASP* 1.3 62.6 + - - +
352C SER 3.1 2.0 - - - -
353C LEU* 2.9 22.8 + - + +
354C GLN* 3.1 42.9 + - + +
287D LEU* 4.6 8.7 - - + +
290D GLY* 4.0 6.3 - - - +
291D MET* 3.6 41.5 - - + +
294D GLU* 4.3 11.7 - - - +
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Residues in contact with ASP 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LYS* 2.7 53.7 + - - +
348C LYS* 3.4 8.5 + - - +
350C VAL* 1.3 78.4 - - - +
352C SER* 1.3 57.3 + - - +
353C LEU 3.0 5.1 + - - -
354C GLN* 4.5 3.3 - - - +
355C LEU* 3.3 56.0 + - + +
360C MET* 4.0 7.7 - - + +
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Residues in contact with SER 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LYS 3.1 12.4 + - - -
349C ARG 3.0 19.2 + - - -
351C ASP* 1.3 74.8 - - - +
353C LEU* 1.3 63.3 + - - +
355C LEU 4.9 2.9 - - - +
360C MET* 4.2 18.6 - - - +
466C ASP* 3.1 38.5 + - - -
467C GLN 5.5 1.3 - - - -
517C ARG* 4.1 5.2 + - - -
519C GLN* 5.1 2.7 - - - -
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Residues in contact with LEU 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ARG 4.0 5.4 - - - +
350C VAL* 2.9 7.0 + - + +
352C SER* 1.3 88.3 - - - +
354C GLN* 1.3 67.7 + - + +
355C LEU 4.6 2.8 - - - +
517C ARG* 3.2 34.3 - - - +
519C GLN* 6.0 2.7 - - + -
287D LEU* 4.0 26.9 - - + -
291D MET* 6.3 1.1 - - - -
310D GLN* 4.8 8.0 + - - +
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Residues in contact with GLN 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C VAL* 3.1 38.8 + - + +
351C ASP* 5.0 1.8 - - - +
353C LEU* 1.3 80.9 - - + +
355C LEU* 1.3 68.5 + - + +
356C THR* 3.5 6.1 + - - +
359C GLN* 4.6 1.4 - - - +
291D MET* 4.1 10.9 - - + +
294D GLU* 3.7 18.8 + - - -
304D LYS* 4.0 21.3 - - - +
309D GLU* 4.5 9.7 - - + +
310D GLN* 3.2 45.8 + - + +
313D HIS* 5.7 2.5 - - - +
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Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ASP* 3.3 48.2 + - + +
352C SER 4.9 0.7 - - - +
353C LEU 4.6 3.0 - - - +
354C GLN* 1.3 83.1 + - + +
356C THR* 1.3 69.7 + - - +
357C ARG 3.8 0.2 + - - -
359C GLN* 3.4 31.6 - - + +
360C MET* 3.8 15.8 - - + +
363C ASN* 3.6 26.7 - - - +
309D GLU* 6.1 0.7 - - - +
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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