Contacts of the helix formed by residues 402 - 425 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309D LEU* 5.9 0.6 - - + +
310D ASP* 4.1 19.5 + - + +
313D ASP* 3.0 18.1 + - - +
400D LEU* 5.1 0.4 - - - -
401D LEU* 1.3 95.1 + - - +
403D VAL* 1.3 64.1 + - - +
404D LYS* 3.6 1.8 - - - -
405D PRO* 3.4 25.7 - - + +
406D ILE* 3.6 13.8 - - - +
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Residues in contact with VAL 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.7 13.2 - - - +
395D GLY* 3.6 18.6 - - - +
400D LEU* 4.4 17.9 - - + +
401D LEU 4.0 1.6 + - - -
402D ASN* 1.3 72.3 - - - +
404D LYS* 1.3 69.4 + - - +
406D ILE* 2.8 22.1 + - - +
407D GLU* 3.0 50.8 + - + +
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Residues in contact with LYS 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D VAL* 1.3 79.5 - - - +
405D PRO* 1.3 71.9 - - + +
407D GLU* 3.4 5.5 + - - +
408D ASP* 3.0 52.5 + - - +
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Residues in contact with PRO 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU* 4.0 22.0 - - + -
402D ASN* 3.4 35.0 - - + +
404D LYS* 1.3 98.9 - - + +
406D ILE* 1.3 60.0 + - - +
408D ASP* 3.4 9.3 + - + +
409D ILE* 3.3 29.6 + - - +
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Residues in contact with ILE 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU* 4.0 21.3 - - + -
313D ASP* 4.4 8.3 - - + -
317D LEU* 4.0 11.9 - - + -
393D LEU* 3.6 41.1 - - + +
394D SER 3.8 2.2 - - - +
395D GLY* 3.8 13.9 - - - +
400D LEU* 3.6 38.1 - - + -
402D ASN 3.6 18.6 - - - +
403D VAL* 2.8 13.2 + - - +
405D PRO* 1.3 69.8 - - - +
407D GLU* 1.3 61.3 + - - +
409D ILE* 3.0 7.3 + - - +
410D GLN* 2.9 24.9 + - - +
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Residues in contact with GLU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.1 26.1 + - - +
417A LYS* 4.6 20.5 + - - -
421A ARG* 4.2 12.5 + - - -
393D LEU 5.3 0.2 - - - -
395D GLY* 4.0 16.8 - - - +
403D VAL* 3.0 32.1 + - + +
404D LYS* 4.1 6.5 + - + +
406D ILE* 1.3 75.3 - - - +
408D ASP* 1.3 58.5 + - - +
410D GLN* 3.8 12.0 - - - +
411D ASP* 2.8 30.1 + - - +
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Residues in contact with ASP 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D LYS* 3.0 54.9 + - - +
405D PRO* 3.6 8.4 - - + +
406D ILE 3.1 0.2 - - - -
407D GLU* 1.3 77.6 - - - +
409D ILE* 1.3 64.3 + - + +
411D ASP* 3.5 16.9 - - - +
412D ASN* 3.6 12.6 + - - +
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Residues in contact with ILE 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ILE* 4.6 3.4 - - + -
304D PRO 3.7 15.9 - - - +
305D GLY* 3.4 37.0 - - - +
306D PHE 4.3 0.2 - - - +
309D LEU* 4.1 9.0 - - + -
393D LEU* 3.8 31.6 - - + -
405D PRO 3.3 15.5 + - - +
406D ILE 3.0 6.4 + - - +
408D ASP* 1.3 77.9 - - + +
410D GLN* 1.3 65.8 + - - +
412D ASN* 3.2 8.7 + - + +
413D LEU* 3.1 29.4 + - + +
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Residues in contact with GLN 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU* 3.7 26.6 - - - +
390D VAL* 3.0 40.9 + - + +
393D LEU* 3.0 25.3 + - + +
394D SER* 3.8 11.9 + - - +
395D GLY 4.5 7.4 + - - -
406D ILE 2.9 11.1 + - - +
407D GLU* 4.0 10.6 - - - +
409D ILE* 1.3 77.5 - - - +
411D ASP* 1.3 56.8 + - - +
413D LEU* 3.6 9.8 - - - +
414D LEU* 2.8 41.5 + - + +
439D MET* 4.2 3.0 - - - +
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Residues in contact with ASP 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLY* 5.1 11.8 + - - -
407D GLU 2.8 19.4 + - - +
408D ASP* 3.5 11.0 - - - +
410D GLN* 1.3 79.2 - - - +
412D ASN* 1.3 69.5 + - - +
414D LEU* 3.3 10.9 + - - +
415D GLN* 2.5 53.7 + - - +
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Residues in contact with ASN 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D PRO* 4.5 21.2 - - - +
211D LEU* 4.0 6.2 - - + +
214D LEU* 4.0 13.9 - - + +
408D ASP 3.6 9.8 + - - +
409D ILE* 3.2 9.9 + - + +
411D ASP* 1.3 85.9 - - - +
413D LEU* 1.3 66.8 + - + +
415D GLN* 3.3 13.5 + - - +
416D ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LEU* 3.9 24.5 - - + -
218D LEU* 3.9 23.3 - - + -
303D ILE* 4.2 10.8 - - + -
386D ILE* 3.6 4.7 - - + +
389D ALA* 3.8 35.0 - - + +
390D VAL* 3.8 14.6 - - + +
393D LEU* 4.0 20.9 - - + -
409D ILE* 3.1 22.2 + - + +
410D GLN* 3.1 7.6 + - - +
412D ASN* 1.3 76.7 - - + +
414D LEU* 1.3 58.3 + - - +
416D ALA* 3.2 5.8 + - - +
417D LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLY* 5.6 2.7 - - - +
416A ALA* 3.9 15.5 - - + -
417A LYS* 5.3 1.6 - - - +
420A LEU* 3.8 25.6 - - + -
390D VAL* 3.8 26.9 - - + -
410D GLN* 2.8 31.8 + - + +
411D ASP* 3.6 10.1 - - - +
412D ASN 3.2 0.2 - - - -
413D LEU* 1.3 77.2 - - - +
415D GLN* 1.3 61.9 + - + +
417D LEU* 3.1 6.3 + - + +
418D GLU* 2.9 24.8 + - - +
432D PHE* 3.7 19.4 - - + -
436D LEU* 4.0 21.5 - - + -
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Residues in contact with GLN 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A PRO* 5.8 9.3 - - + +
413A GLY* 5.9 9.0 - - - +
206D PRO 2.7 35.2 - - - +
211D LEU* 3.8 18.3 - - + +
411D ASP* 2.5 37.9 + - - +
412D ASN* 3.6 11.4 + - - +
414D LEU* 1.3 77.4 - - + +
416D ALA* 1.3 62.5 + - - +
418D GLU* 3.4 9.5 + - - +
419D LEU* 3.1 24.3 + - - +
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Residues in contact with ALA 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU* 3.8 31.6 - - + +
212D ARG* 4.6 1.6 + - - -
214D LEU* 3.9 19.5 - - + -
215D ALA* 5.0 0.8 - - - +
386D ILE* 3.8 14.9 - - + +
412D ASN 3.0 14.1 + - - +
413D LEU 3.2 8.7 + - - +
415D GLN* 1.3 77.8 - - - +
417D LEU* 1.3 56.9 + - - +
419D LEU* 3.4 2.1 + - - +
420D GLN* 2.9 30.7 + - - +
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ASP* 4.0 13.0 - - - +
386D ILE* 3.7 30.0 - - + +
387D PHE* 4.1 9.6 - - + +
390D VAL* 4.1 18.4 - - + -
413D LEU 2.9 14.3 + - - +
414D LEU* 3.1 9.2 + - + +
416D ALA* 1.3 74.3 - - - +
418D GLU* 1.3 59.3 + - - +
420D GLN* 3.5 1.4 - - + +
421D LEU* 2.9 50.4 + - + +
432D PHE* 3.9 16.6 - - + -
435D LEU* 4.1 27.4 - - + -
436D LEU* 4.3 13.0 - - + -
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Residues in contact with GLU 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A GLU* 4.2 14.8 - - - +
405A LYS* 5.2 2.9 + - - -
412A PRO 5.2 5.4 - - - +
415A PHE* 6.3 0.7 - - - -
414D LEU 2.9 15.8 + - - +
415D GLN* 3.7 9.1 - - - +
417D LEU* 1.3 77.4 - - - +
419D LEU* 1.3 57.7 + - - +
421D LEU* 3.2 4.6 + - - +
422D LYS* 2.8 63.5 + - + +
432D PHE* 3.4 47.4 - - + +
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Residues in contact with LEU 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D SER* 4.0 20.6 - - - +
211D LEU* 3.5 32.3 - - + -
212D ARG* 3.4 33.9 - - + +
415D GLN 3.1 14.4 + - - +
416D ALA 3.7 3.6 - - - +
418D GLU* 1.3 78.1 - - - +
420D GLN* 1.3 64.0 + - - +
422D LYS* 3.0 11.1 + - + -
423D LEU* 2.9 55.5 + - + +
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Residues in contact with GLN 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ARG* 3.2 36.9 + - - +
215D ALA* 4.4 6.2 - - - +
382D SER* 3.4 29.8 + - - -
383D ASP* 2.8 32.4 + - - +
386D ILE* 3.3 23.1 - - + -
416D ALA 2.9 19.0 + - - +
417D LEU* 3.5 5.6 - - + +
418D GLU 3.3 0.2 - - - -
419D LEU* 1.3 75.5 - - - +
421D LEU* 1.3 59.8 + - + +
423D LEU* 4.1 0.7 - - - +
424D ASN* 2.9 53.7 + - - +
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Residues in contact with LEU 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D LEU* 5.4 2.2 - - + -
383D ASP* 4.1 21.1 - - + +
417D LEU* 2.9 38.1 + - + +
418D GLU* 3.6 3.8 - - - +
420D GLN* 1.3 74.1 - - - +
422D LYS* 1.3 62.0 + - + +
424D ASN 4.5 0.2 - - - +
425D HIS* 2.8 40.6 + - + +
431D LEU* 3.8 28.0 - - + +
432D PHE* 3.5 47.8 - - + +
435D LEU* 4.2 19.3 - - + -
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Residues in contact with LYS 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A LYS* 5.3 8.0 - - - +
418D GLU* 2.8 51.4 + - + +
419D LEU* 3.0 11.4 + - + +
421D LEU* 1.3 76.8 - - + +
423D LEU* 1.3 70.5 + - + +
425D HIS 4.8 2.0 - - - -
426D PRO* 3.3 26.5 - - - +
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Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ARG* 3.5 47.1 - - + +
419D LEU* 2.9 36.8 + - + +
420D GLN* 4.1 2.7 - - - +
422D LYS* 1.3 84.2 - - + +
424D ASN* 1.3 60.4 + - - +
426D PRO* 3.6 10.7 - - - +
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Residues in contact with ASN 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D ASP* 2.9 28.5 + - - +
382D SER* 4.8 0.7 - - - -
383D ASP* 3.1 23.8 + - - -
420D GLN* 2.9 35.7 + - - +
423D LEU* 1.3 77.3 - - + +
425D HIS* 1.3 77.6 + - + +
426D PRO* 3.7 4.0 - - - +
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Residues in contact with HIS 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D LEU 4.4 4.9 + - - -
378D GLU* 3.3 28.4 + - + -
379D LEU* 4.3 1.4 - - - -
380D ASP* 5.0 0.6 + - - -
383D ASP* 2.9 31.4 + - - -
421D LEU* 2.8 23.9 + - + +
422D LYS* 4.8 1.0 - - - -
424D ASN* 1.3 104.8 + - + +
426D PRO* 1.3 67.2 - - - +
427D GLU 3.3 2.5 - - - -
428D SER* 3.1 37.0 + - - +
431D LEU* 3.6 22.5 - - + +
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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