Contacts of the helix formed by residues 402 - 425 (chain X) in PDB entry 1FM6
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 402 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309X LEU* 5.2 0.6 - - + +
310X ASP* 4.4 18.2 + - + +
313X ASP* 2.8 18.1 + - - +
400X LEU* 5.5 0.2 - - - -
401X LEU* 1.3 85.7 + - - +
403X VAL* 1.3 63.8 + - - +
404X LYS* 3.5 2.2 - - - -
405X PRO* 3.2 28.2 - - + +
406X ILE* 3.5 14.8 - - - +
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Residues in contact with VAL 403 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356U LYS* 4.0 11.7 - - - +
395X GLY* 3.7 20.4 - - - +
400X LEU* 4.4 23.8 - - + +
401X LEU 3.8 3.6 + - - +
402X ASN* 1.3 70.5 - - - +
404X LYS* 1.3 58.5 - - - +
406X ILE* 2.7 33.2 + - - +
407X GLU* 2.9 48.0 + - + +
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Residues in contact with LYS 404 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402X ASN 5.2 0.2 - - - -
403X VAL* 1.3 79.7 - - - +
405X PRO* 1.3 70.9 - - + +
407X GLU* 3.4 7.0 + - - +
408X ASP* 2.8 52.5 + - - +
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Residues in contact with PRO 405 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308X ASN* 6.2 0.2 - - - +
309X LEU* 3.9 20.0 - - + -
402X ASN* 3.2 34.5 - - + +
404X LYS* 1.3 98.3 - - + +
406X ILE* 1.3 56.0 + - - +
408X ASP* 3.7 9.6 + - + +
409X ILE* 3.0 31.3 + - + +
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Residues in contact with ILE 406 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309X LEU* 3.9 22.0 - - + -
313X ASP* 4.1 10.3 - - + -
317X LEU* 3.5 25.1 - - + -
393X LEU* 3.9 30.1 - - + +
394X SER 3.9 9.2 - - - +
395X GLY* 3.9 6.5 - - - -
400X LEU* 3.7 28.5 - - + -
402X ASN 3.5 18.8 - - - +
403X VAL* 2.7 15.1 + - - +
405X PRO* 1.3 70.9 - - - +
407X GLU* 1.3 65.0 + - - +
409X ILE* 3.0 8.0 + - - +
410X GLN* 3.0 19.9 + - - +
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Residues in contact with GLU 407 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356U LYS* 3.7 21.7 - - - +
417U LYS* 4.3 24.1 + - - +
421U ARG* 4.1 12.1 + - - -
393X LEU 5.2 0.2 - - - -
395X GLY* 3.9 16.5 + - - +
403X VAL* 2.9 40.5 + - + +
404X LYS* 4.1 6.4 + - - +
406X ILE* 1.3 75.5 - - - +
408X ASP* 1.3 64.2 + - - +
410X GLN* 3.3 12.2 + - - +
411X ASP* 3.0 24.8 + - - +
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Residues in contact with ASP 408 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404X LYS* 2.8 55.6 + - - +
405X PRO* 3.9 9.3 - - + +
406X ILE 3.2 0.2 - - - -
407X GLU* 1.3 78.6 - - - +
409X ILE* 1.3 62.6 + - + +
411X ASP* 3.7 12.4 + - - +
412X ASN* 3.6 17.9 + - - -
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Residues in contact with ILE 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303X ILE* 4.6 2.9 - - + -
304X PRO 3.6 17.3 - - - +
305X GLY* 3.8 34.1 - - - +
308X ASN* 5.0 1.3 - - - +
309X LEU* 4.2 11.9 - - + -
393X LEU* 3.4 33.4 - - + -
405X PRO* 3.0 17.9 + - + +
406X ILE 3.0 2.1 + - - +
408X ASP* 1.3 76.8 - - + +
410X GLN* 1.3 64.4 + - - +
412X ASN* 3.2 19.8 + - + +
413X LEU* 3.2 21.8 + - + +
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Residues in contact with GLN 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420U LEU* 3.9 19.7 - - - +
421U ARG* 5.9 0.7 + - - -
390X VAL* 2.8 40.8 + - + +
393X LEU* 3.0 28.1 + - + +
394X SER* 3.7 12.9 + - - +
395X GLY 4.7 3.5 + - - -
406X ILE 3.0 8.5 + - - +
407X GLU* 3.3 13.4 + - - +
409X ILE* 1.3 73.5 - - - +
411X ASP* 1.3 55.6 + - - +
413X LEU* 3.1 11.0 + - - +
414X LEU* 2.7 52.0 + - + +
439X MET* 4.6 3.2 - - - +
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Residues in contact with ASP 411 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413U GLY* 4.2 20.6 + - - +
407X GLU 3.0 16.6 + - - +
408X ASP* 3.7 9.5 - - - +
409X ILE 3.2 0.2 - - - -
410X GLN* 1.3 76.8 - - - +
412X ASN* 1.3 60.7 + - - +
414X LEU* 3.4 11.3 + - - +
415X GLN* 2.5 62.8 + - - +
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Residues in contact with ASN 412 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206X PRO* 4.1 17.8 - - - +
211X LEU* 4.2 7.7 - - + +
214X LEU* 4.2 12.3 - - + +
408X ASP 3.6 15.5 + - - -
409X ILE* 3.2 13.1 + - + +
411X ASP* 1.3 79.7 - - - +
413X LEU* 1.3 53.4 + - + +
415X GLN* 3.3 15.2 + - - +
416X ALA* 2.8 34.4 + - - +
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Residues in contact with LEU 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214X LEU* 3.9 15.3 - - + -
218X LEU* 3.8 29.2 - - + -
303X ILE* 4.4 11.7 - - + -
304X PRO* 5.9 0.2 - - + -
386X ILE* 3.6 5.0 - - + +
389X ALA* 3.5 35.0 - - + +
390X VAL* 3.8 16.2 - - + +
393X LEU* 3.7 19.7 - - + -
409X ILE* 3.5 17.0 - - + +
410X GLN* 3.1 11.6 + - - +
412X ASN* 1.3 78.8 - - + +
414X LEU* 1.3 54.3 + - - +
416X ALA* 3.1 6.4 + - - +
417X LEU* 2.6 35.9 + - - +
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Residues in contact with LEU 414 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413U GLY 5.9 0.4 - - - +
416U ALA* 4.2 11.9 - - + -
417U LYS* 5.6 1.1 - - - +
420U LEU* 3.7 24.2 - - + -
390X VAL* 3.8 20.0 - - + -
410X GLN* 2.7 39.4 + - + +
411X ASP* 3.7 10.3 - - - +
413X LEU* 1.3 68.9 - - - +
415X GLN* 1.3 57.1 + - + +
417X LEU* 3.0 6.7 + - + +
418X GLU* 2.7 35.7 + - - +
432X PHE* 3.7 20.3 - - + -
436X LEU* 3.7 32.1 - - + -
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Residues in contact with GLN 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412U PRO* 5.9 8.8 - - + +
413U GLY* 5.8 5.4 - - - -
206X PRO* 3.8 27.6 - - - +
211X LEU* 4.1 16.5 - - + +
411X ASP* 2.5 56.3 + - - +
412X ASN* 3.5 16.2 + - - +
414X LEU* 1.3 75.8 - - + +
416X ALA* 1.3 63.0 + - - +
418X GLU* 3.3 12.4 + - - +
419X LEU* 3.1 23.9 + - - +
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Residues in contact with ALA 416 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X LEU* 3.7 31.7 - - + +
212X ARG* 4.8 2.1 + - - -
214X LEU* 3.8 23.1 - - + -
215X ALA 5.0 0.4 - - - +
386X ILE* 4.0 13.2 - - + +
412X ASN 2.8 18.0 + - - +
413X LEU* 3.4 5.8 - - - +
415X GLN* 1.3 77.1 - - - +
417X LEU* 1.3 57.8 + - - +
419X LEU* 3.5 2.1 + - - +
420X GLN* 3.0 29.3 + - - +
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Residues in contact with LEU 417 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383X ASP 4.5 4.7 - - - +
386X ILE* 3.7 27.3 - - + +
387X PHE* 4.4 19.3 - - + +
390X VAL* 3.9 20.9 - - + -
413X LEU 2.6 21.3 + - - +
414X LEU* 3.2 4.9 - - + +
416X ALA* 1.3 71.5 - - - +
418X GLU* 1.3 66.7 + - - +
420X GLN* 3.2 2.5 + - + +
421X LEU* 2.9 49.5 + - + +
432X PHE* 3.8 21.3 - - + -
435X LEU* 4.2 12.1 - - + -
436X LEU* 4.3 13.9 - - + -
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Residues in contact with GLU 418 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401U GLU* 4.0 15.9 - - - +
405U LYS* 4.8 8.5 + - - -
412U PRO 5.1 6.2 - - - +
413U GLY* 6.1 0.3 - - - -
415U PHE* 6.3 0.4 - - - -
414X LEU 2.7 18.7 + - - +
415X GLN* 3.7 10.6 - - - +
417X LEU* 1.3 74.8 - - - +
419X LEU* 1.3 58.0 + - - +
421X LEU* 3.3 4.5 + - - +
422X LYS* 2.9 30.7 + - + +
432X PHE* 3.7 46.3 - - + -
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Residues in contact with LEU 419 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208X SER* 3.9 17.9 - - - +
211X LEU* 3.5 32.8 - - + -
212X ARG* 3.5 32.1 - - + -
415X GLN 3.1 16.4 + - - +
416X ALA 3.8 4.3 - - - +
418X GLU* 1.3 76.8 - - - +
420X GLN* 1.3 61.9 + - - +
422X LYS* 3.4 8.0 + - + +
423X LEU* 3.0 40.1 + - + +
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Residues in contact with GLN 420 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212X ARG* 3.0 36.9 + - - +
215X ALA* 4.1 7.8 - - - +
382X SER* 3.5 21.1 + - - -
383X ASP* 2.9 32.0 + - - +
386X ILE* 3.5 23.3 - - + +
416X ALA 3.0 18.8 + - - +
417X LEU* 3.2 4.9 + - + +
419X LEU* 1.3 76.5 - - - +
421X LEU* 1.3 56.0 + - + +
423X LEU* 3.3 0.5 + - - +
424X ASN* 2.7 64.6 + - - +
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Residues in contact with LEU 421 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379X LEU* 4.3 8.7 - - + -
383X ASP* 4.1 26.7 - - + +
417X LEU* 2.9 36.2 + - + +
418X GLU* 3.7 4.3 - - - +
420X GLN* 1.3 76.7 - - + +
422X LYS* 1.3 58.0 + - - +
425X HIS* 3.1 36.2 + - + +
431X LEU* 4.1 27.2 - - + +
432X PHE* 3.6 40.2 - - + +
435X LEU* 3.9 15.5 - - + -
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Residues in contact with LYS 422 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418X GLU* 2.9 18.2 + - + +
419X LEU* 3.8 11.4 - - + +
420X GLN 3.2 0.2 - - - -
421X LEU* 1.3 77.2 - - - +
423X LEU* 1.3 64.1 + - + +
425X HIS 4.7 1.6 - - - -
426X PRO* 3.2 48.3 + - - +
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Residues in contact with LEU 423 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212X ARG* 3.4 46.0 - - + +
419X LEU* 3.0 32.8 + - + +
420X GLN* 3.9 2.5 - - - +
422X LYS* 1.3 82.4 - - + +
424X ASN* 1.3 61.1 + - + +
426X PRO* 3.7 9.9 - - - +
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Residues in contact with ASN 424 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380X ASP* 2.9 26.0 + - - +
382X SER* 4.5 1.6 + - - -
383X ASP* 3.2 7.9 + - - -
420X GLN* 2.7 39.7 + - - +
423X LEU* 1.3 74.5 - - - +
425X HIS* 1.3 93.0 + - + +
426X PRO* 3.5 5.4 - - - +
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Residues in contact with HIS 425 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377X LEU 5.0 1.8 + - - -
378X GLU* 3.2 29.4 + - - +
379X LEU* 4.3 1.8 - - - +
380X ASP* 4.9 2.5 - - - -
383X ASP* 2.8 29.9 + - - -
421X LEU* 3.1 23.9 + - + +
422X LYS* 4.7 0.9 - - - -
424X ASN* 1.3 102.4 + - + +
426X PRO* 1.3 65.2 - - - +
427X GLU 3.3 3.1 - - - +
428X SER* 3.1 32.4 + - - +
431X LEU* 3.8 20.1 - - + +
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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
------------------------------------------------------------
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