Contacts of the helix formed by residues 385 - 408 (chain C) in PDB entry 1XV9
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 385 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C PRO* 5.3 5.0 - - + +
296C ASP* 3.6 14.4 + - - +
383C LEU* 3.3 4.2 - - - -
384C SER* 1.3 82.6 + - - +
386C PRO* 1.3 62.8 - - - +
387C ALA* 3.1 9.0 - - - +
388C GLU* 2.8 47.2 + - - +
389C VAL* 3.5 17.8 + - - +
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Residues in contact with PRO 386 (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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378C PRO* 3.9 13.1 - - + +
383C LEU* 3.1 40.6 - - + +
384C SER 3.5 4.0 - - - +
385C ASN* 1.3 88.1 - - - +
387C ALA* 1.3 69.3 + - + +
389C VAL* 3.3 3.7 + - + +
390C GLU* 3.0 20.7 + - - +
244D HIS* 6.5 0.7 - - + -
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Residues in contact with ALA 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ASN* 3.1 9.2 - - - +
386C PRO* 1.3 85.2 - - + +
388C GLU* 1.3 66.9 + - - +
389C VAL 2.9 0.3 + - - -
390C GLU* 2.9 13.7 + - - +
391C ALA* 3.0 12.8 + - - +
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Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLU* 4.1 10.9 - - - +
292C LEU* 3.0 33.1 - - + +
293C PRO* 3.9 15.5 - - - +
385C ASN* 2.8 40.1 + - + +
387C ALA* 1.3 73.1 - - - +
389C VAL* 1.3 57.7 + - + +
391C ALA* 3.0 11.0 + - + +
392C LEU* 2.9 37.5 + - + +
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Residues in contact with VAL 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU* 4.7 8.5 - - + -
296C ASP* 5.6 3.6 - - + -
300C LEU* 3.9 22.2 - - + -
376C PHE* 3.8 7.8 - - + +
377C ASN 3.7 15.9 - - - +
378C PRO* 3.5 30.3 - - + -
383C LEU* 4.0 17.5 - - + -
385C ASN 3.5 13.0 + - - +
386C PRO 3.4 8.3 - - - +
387C ALA 2.9 0.8 + - - -
388C GLU* 1.3 79.9 - - + +
390C GLU* 1.3 59.2 + - - +
392C LEU* 3.1 11.9 + - - +
393C ARG* 2.8 25.3 + - - +
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Residues in contact with GLU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C PRO* 3.8 24.4 - - + +
386C PRO 3.0 5.0 + - - +
387C ALA* 2.9 12.0 + - - +
389C VAL* 1.3 75.3 - - - +
391C ALA* 1.3 59.1 + - - +
393C ARG* 3.7 19.3 + - - +
394C GLU* 2.9 35.9 + - + +
311D LYS* 3.9 25.3 + - - +
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Residues in contact with ALA 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C ALA 3.0 10.9 + - - +
388C GLU* 3.1 15.3 - - - +
390C GLU* 1.3 75.7 - - - +
392C LEU* 1.3 66.6 + - + +
394C GLU* 3.0 17.9 + - - +
395C LYS* 3.0 23.6 + - - +
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C MET* 3.6 6.3 - - + +
288C HIS* 3.7 32.3 - - + +
292C LEU* 3.4 45.3 - - + -
376C PHE* 3.7 24.5 - - + -
388C GLU* 2.9 24.6 + - + +
389C VAL* 3.4 6.3 - - - +
391C ALA* 1.3 78.4 - - + +
393C ARG* 1.3 57.5 + - - +
394C GLU 3.0 0.2 - - - -
395C LYS* 2.8 47.6 + - + +
396C VAL* 3.1 9.2 + - - +
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Residues in contact with ARG 393 (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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373C ILE* 4.0 21.1 + - + +
376C PHE* 2.8 43.2 - - + +
377C ASN* 4.0 11.8 + - - -
378C PRO* 3.3 31.0 - - - +
379C ASP* 5.0 4.2 + - - -
389C VAL 2.8 15.6 + - - +
390C GLU* 3.9 15.0 + - - +
392C LEU* 1.3 72.5 - - - +
394C GLU* 1.3 59.3 + - - +
396C VAL* 3.6 7.0 + - - +
397C TYR* 3.0 62.8 + - + -
311D LYS* 4.2 14.2 + - - +
314D GLY* 4.0 24.2 - - - -
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Residues in contact with GLU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C GLU* 2.9 32.2 + - + +
391C ALA* 3.1 15.5 - - - +
392C LEU 3.0 0.2 - - - -
393C ARG* 1.3 77.6 - - - +
395C LYS* 1.3 61.2 + - - +
397C TYR* 3.0 41.0 + - - +
398C ALA* 3.2 7.4 + - - +
305D ASP* 4.9 1.7 - - - +
306D ARG* 4.1 11.3 - - - +
307D PHE* 3.6 23.6 - - - -
311D LYS* 3.2 34.8 + - - +
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Residues in contact with LYS 395 (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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227C ASN 4.7 0.5 + - - -
229C ASP* 3.0 47.3 + - + +
230C MET* 3.8 19.7 - - + -
288C HIS* 4.2 13.5 + - + -
391C ALA* 3.0 19.6 + - - +
392C LEU* 2.8 30.7 + - + +
394C GLU* 1.3 76.4 - - - +
396C VAL* 1.3 55.9 + - - +
398C ALA* 3.1 10.8 + - - +
399C SER* 3.0 29.5 + - - -
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Residues in contact with VAL 396 (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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230C MET* 3.4 39.3 - - + -
235C ILE* 4.7 2.2 - - + -
369C CYS* 3.3 37.9 - - + +
372C ALA* 3.9 18.8 - - + -
373C ILE* 3.4 14.8 - - + +
376C PHE* 4.2 7.0 - - + -
392C LEU 3.1 5.0 + - - +
393C ARG* 3.9 9.6 - - - +
394C GLU 3.2 0.2 - - - -
395C LYS* 1.3 72.0 - - - +
397C TYR* 1.3 61.6 + - - +
398C ALA 3.1 1.8 - - - -
399C SER* 4.1 2.5 - - - +
400C LEU* 3.1 25.5 + - - +
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Residues in contact with TYR 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C ILE* 4.0 25.8 - - + +
393C ARG* 3.0 65.8 + - + -
394C GLU* 3.0 28.4 + - - +
396C VAL* 1.3 78.9 - - - +
398C ALA* 1.3 59.9 + - - +
400C LEU 4.2 0.2 - - - -
401C GLU* 3.7 7.3 + - - +
415C PHE* 3.4 30.4 - + - -
419C LEU* 4.2 9.2 - - + -
422C LEU* 5.7 2.5 - - + +
307D PHE* 3.1 36.5 - + + -
310D ALA* 3.1 45.4 + - + -
311D LYS* 3.7 3.8 + - + -
314D GLY* 5.4 0.3 + - - -
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Residues in contact with ALA 398 (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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227C ASN* 4.1 22.2 - - - +
394C GLU 3.2 6.0 + - - +
395C LYS* 3.1 16.3 + - - +
397C TYR* 1.3 75.4 - - - +
399C SER* 1.3 66.7 + - - +
400C LEU 3.1 0.9 - - - -
401C GLU* 3.0 5.6 + - - +
402C ALA* 2.8 24.7 + - - +
306D ARG* 5.2 11.2 - - - +
307D PHE* 3.8 9.8 - - + -
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Residues in contact with SER 399 (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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227C ASN 2.7 21.4 + - - +
230C MET* 2.6 46.4 + - - +
232C VAL* 3.4 17.7 - - - +
235C ILE* 5.2 0.9 - - - -
369C CYS* 5.0 4.3 - - - -
395C LYS 3.0 5.0 + - - -
396C VAL* 4.5 3.6 - - - -
398C ALA* 1.3 76.2 - - - +
400C LEU* 1.3 58.3 + - - +
402C ALA* 3.5 4.7 - - - +
403C TYR* 2.9 32.4 + - - +
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Residues in contact with LEU 400 (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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366C GLU* 4.1 13.9 - - + -
369C CYS* 3.6 32.0 - - + -
370C LEU* 3.1 36.3 - - + +
373C ILE* 4.0 10.5 - - + -
396C VAL 3.1 18.7 + - - +
398C ALA 3.1 1.0 - - - -
399C SER* 1.3 75.5 - - - +
401C GLU* 1.3 59.3 + - - +
403C TYR* 4.8 4.7 - - + -
404C CYS* 2.8 27.2 + - - +
415C PHE* 3.8 17.9 - - + -
418C LEU* 3.4 26.2 - - + -
419C LEU* 4.5 0.2 - - + -
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Residues in contact with GLU 401 (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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397C TYR 3.7 14.1 + - - +
398C ALA* 3.0 4.6 + - - +
400C LEU* 1.3 77.0 - - - +
402C ALA* 1.3 62.2 + - - +
404C CYS* 3.5 5.6 - - + +
405C LYS* 2.8 56.0 + - + +
415C PHE* 3.9 33.2 - - + +
297D LYS* 5.1 9.9 + - - -
306D ARG* 4.3 11.1 + - - -
307D PHE* 4.0 15.2 - - - -
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Residues in contact with ALA 402 (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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227C ASN* 3.6 22.2 - - - +
232C VAL* 5.8 1.1 - - + -
398C ALA 2.8 16.0 + - - +
399C SER* 3.5 7.4 - - - +
401C GLU* 1.3 80.9 - - - +
403C TYR* 1.3 66.2 + - - +
405C LYS* 3.7 2.3 - - - +
406C HIS* 2.9 23.6 + - - +
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Residues in contact with TYR 403 (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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232C VAL* 4.0 20.4 - - + +
363C ASP* 2.7 24.8 + - - -
365C THR* 3.4 33.2 + - + -
366C GLU* 3.4 29.6 - - + -
369C CYS* 5.9 0.2 - - - -
399C SER 2.9 19.7 + - - +
400C LEU* 4.5 7.6 - - + +
402C ALA* 1.3 73.1 - - - +
404C CYS* 1.3 61.9 + - - +
406C HIS* 4.3 10.1 - + - -
407C LYS* 3.0 67.6 + - + +
408C TYR* 3.7 9.8 + + - -
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Residues in contact with CYS 404 (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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366C GLU* 3.4 22.4 - - - -
400C LEU 2.8 24.0 + - - +
401C GLU* 3.5 10.8 - - + +
402C ALA 3.0 0.6 - - - -
403C TYR* 1.3 81.2 - - - +
405C LYS* 1.3 59.3 + - + +
408C TYR* 3.0 34.1 + - - +
414C ARG* 3.9 17.7 - - - +
415C PHE* 4.1 21.1 - - + -
418C LEU* 3.7 17.7 - - - -
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Residues in contact with LYS 405 (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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401C GLU* 2.8 48.8 + - + +
402C ALA* 3.9 2.7 - - - +
404C CYS* 1.3 71.9 - - + +
406C HIS* 1.3 63.7 + - - +
408C TYR 4.5 0.2 - - - -
409C PRO* 2.7 44.0 - - + +
411C GLN 5.0 3.1 + - - +
412C PRO* 3.5 26.9 + - - +
413C GLY* 5.1 1.8 - - - -
415C PHE* 5.7 4.7 - - - +
297D LYS* 5.9 3.4 - - - +
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Residues in contact with HIS 406 (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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402C ALA 2.9 17.3 + - - +
403C TYR* 3.9 11.2 - + - +
405C LYS* 1.3 81.3 - - - +
407C LYS* 1.3 100.6 + - + +
409C PRO* 3.0 15.1 - - - +
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Residues in contact with LYS 407 (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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403C TYR* 3.0 51.0 + - + +
406C HIS* 1.3 103.3 + - + +
408C TYR* 1.3 83.1 + - + +
409C PRO* 3.1 12.1 - - - +
410C GLU* 3.6 4.9 - - - +
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Residues in contact with TYR 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C GLN* 4.1 11.5 + - + +
363C ASP* 2.3 36.0 + - - +
366C GLU* 3.8 23.6 - - - -
403C TYR* 3.5 6.7 + + - -
404C CYS 3.0 22.6 + - - +
405C LYS* 4.6 1.4 - - - +
407C LYS* 1.3 104.9 - - + +
409C PRO* 1.3 54.9 - - - +
410C GLU* 2.9 23.2 + - - -
411C GLN* 3.1 50.9 + - + +
414C ARG* 3.7 17.5 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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