Contacts of the helix formed by residues 385 - 408 (chain U) 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 385 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293U PRO* 6.3 0.7 - - + -
296U ASP* 4.6 4.6 + - - +
383U LEU* 2.9 7.6 + - - +
384U SER* 1.3 87.8 + - - +
386U PRO* 1.3 69.5 - - - +
387U ALA* 3.6 12.2 + - - +
388U GLU* 2.9 49.2 + - + +
389U VAL* 3.6 10.7 + - - +
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Residues in contact with PRO 386 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378U PRO* 3.7 30.8 - - + +
380U SER 5.6 0.9 - - - +
383U LEU* 3.7 22.2 - - + +
384U SER 4.4 0.2 - - - -
385U ASN* 1.3 86.9 - - - +
387U ALA* 1.3 53.4 + - - +
389U VAL* 2.9 6.6 + - - +
390U GLU* 2.8 36.0 + - - +
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Residues in contact with ALA 387 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385U ASN* 3.3 10.0 + - - +
386U PRO* 1.3 79.6 - - + +
388U GLU* 1.3 60.7 + - - +
390U GLU* 3.5 10.6 - - - +
391U ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 388 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291U GLU* 6.1 0.3 - - - +
292U LEU* 3.8 28.0 + - + +
293U PRO* 4.4 11.8 - - - +
385U ASN* 2.9 37.3 + - - +
386U PRO 3.1 1.0 - - - -
387U ALA* 1.3 76.0 - - - +
389U VAL* 1.3 72.9 + - + +
391U ALA* 3.2 7.9 + - - +
392U LEU* 3.2 29.8 + - + +
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Residues in contact with VAL 389 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292U LEU* 4.1 16.6 - - + -
296U ASP* 5.6 2.5 - - + -
300U LEU* 4.1 25.8 - - + -
376U PHE* 3.4 36.2 - - + +
377U ASN 3.8 3.8 - - - +
378U PRO* 3.6 18.2 - - + -
383U LEU* 4.5 11.0 - - + -
385U ASN 3.6 7.3 + - - +
386U PRO 2.9 7.2 + - - +
388U GLU* 1.3 81.7 - - + +
390U GLU* 1.3 58.4 + - - +
392U LEU* 3.1 10.6 + - - +
393U ARG* 2.9 25.8 + - - +
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Residues in contact with GLU 390 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378U PRO* 3.1 32.9 - - + +
386U PRO 2.8 15.8 + - - +
387U ALA* 3.5 11.7 - - - +
388U GLU 3.2 0.2 - - - -
389U VAL* 1.3 77.5 - - - +
391U ALA* 1.3 62.0 + - - +
393U ARG* 3.3 11.6 + - - +
394U GLU* 2.9 59.7 + - - +
397U TYR* 5.2 1.4 - - - -
434X LYS* 4.6 7.3 - - - +
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Residues in contact with ALA 391 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387U ALA 3.1 14.1 + - - +
388U GLU* 3.2 10.7 + - - +
390U GLU* 1.3 74.9 - - - +
392U LEU* 1.3 66.8 + - + +
394U GLU* 3.5 11.2 + - - +
395U LYS* 3.1 39.8 + - - +
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Residues in contact with LEU 392 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230U MET* 4.5 5.9 - - + +
288U HIS* 3.8 38.1 - - + +
292U LEU* 3.9 19.5 - - + -
376U PHE* 3.3 46.9 - - + -
388U GLU* 3.2 25.6 + - + +
389U VAL* 3.1 9.7 + - - +
391U ALA* 1.3 77.1 - - + +
393U ARG* 1.3 65.2 + - - +
395U LYS* 3.0 28.0 + - + +
396U VAL* 3.1 15.6 + - - +
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Residues in contact with ARG 393 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373U ILE* 2.8 37.2 + - + +
374U VAL* 4.0 5.5 + - - +
376U PHE* 2.9 28.1 + - - +
377U ASN* 3.4 30.1 + - - +
378U PRO* 3.7 16.7 - - - +
379U ASP* 5.6 2.4 + - - -
389U VAL 2.9 6.9 + - - +
390U GLU* 3.5 17.7 + - - +
392U LEU* 1.3 76.9 - - - +
394U GLU* 1.3 57.2 + - - +
396U VAL* 3.0 13.3 + - - +
397U TYR* 2.9 52.5 + - + -
426U ARG* 5.1 6.3 - - - +
437X GLN* 3.7 31.6 + - - +
441X ASP* 5.9 0.2 + - - -
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Residues in contact with GLU 394 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390U GLU* 2.9 40.2 + - - +
391U ALA* 3.8 8.5 - - - +
393U ARG* 1.3 73.0 - - - +
395U LYS* 1.3 61.4 + - + +
397U TYR* 3.5 19.5 - - + -
398U ALA 2.9 10.9 + - - -
429X SER* 4.8 4.0 + - - +
430X GLN* 2.5 47.6 + - - +
434X LYS* 2.9 35.2 + - + -
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Residues in contact with LYS 395 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 6.3 0.4 - - - +
228U GLU* 5.1 1.8 - - - +
229U ASP* 3.3 50.7 + - + +
230U MET* 3.7 6.5 - - + +
288U HIS* 5.5 6.6 + - + -
391U ALA* 3.1 27.5 + - - +
392U LEU* 3.0 24.7 + - + +
394U GLU* 1.3 76.9 - - + +
396U VAL* 1.3 58.4 + - - +
398U ALA* 3.5 6.7 + - - +
399U SER* 2.9 31.7 + - - -
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Residues in contact with VAL 396 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230U MET* 3.8 26.2 - - - -
235U ILE* 4.8 3.8 - - + -
369U CYS* 3.3 41.7 - - + +
372U ALA* 4.1 17.7 - - + -
373U ILE* 3.5 13.5 - - + -
376U PHE* 4.3 9.6 - - + -
392U LEU 3.1 13.7 + - - +
393U ARG* 3.0 9.3 + - - +
395U LYS* 1.3 75.4 - - - +
397U TYR* 1.3 64.5 + - - +
399U SER* 4.4 3.1 - - - -
400U LEU* 2.8 23.9 + - - +
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Residues in contact with TYR 397 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373U ILE* 3.7 34.1 - - + -
390U GLU* 5.2 1.3 - - - -
393U ARG* 2.9 31.6 + - + -
394U GLU* 3.4 27.4 - - + +
396U VAL* 1.3 75.7 - - - +
398U ALA* 1.3 58.8 + - - +
400U LEU* 4.8 0.7 - - - -
401U GLU* 3.0 25.9 + - - +
415U PHE* 3.2 17.3 - + + -
419U LEU* 4.1 15.5 - - + -
430X GLN* 3.7 11.0 - - + +
433X ALA* 3.7 39.0 - - + -
434X LYS* 4.3 13.6 - - + -
437X GLN* 2.9 36.8 + - - +
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Residues in contact with ALA 398 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228U GLU* 5.0 8.5 - - - +
394U GLU 2.9 9.7 + - - +
395U LYS* 3.6 7.9 - - - +
397U TYR* 1.3 78.2 - - - +
399U SER* 1.3 61.1 + - - +
401U GLU* 3.5 9.7 + - - +
402U ALA* 3.1 24.6 + - - +
430X GLN* 3.2 21.3 - - + +
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Residues in contact with SER 399 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228U GLU* 3.2 19.0 + - - -
230U MET* 2.5 37.9 + - - +
232U VAL* 3.8 17.8 + - - +
235U ILE* 5.7 1.6 - - - -
369U CYS* 5.6 0.7 - - - -
395U LYS 2.9 14.8 + - - -
396U VAL* 3.8 4.9 - - - -
398U ALA* 1.3 74.2 - - - +
400U LEU* 1.3 61.4 + - - +
402U ALA* 3.5 6.6 + - - +
403U TYR* 3.0 27.5 + - - +
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Residues in contact with LEU 400 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232U VAL* 4.6 0.4 - - - +
366U GLU* 4.0 20.0 - - + -
369U CYS* 3.5 38.8 - - + -
370U LEU* 4.3 23.6 - - + -
373U ILE* 4.5 9.2 - - + -
396U VAL 2.8 17.0 + - - +
397U TYR 3.9 2.5 - - - +
399U SER* 1.3 73.6 - - - +
401U GLU* 1.3 68.1 + - - +
403U TYR* 3.1 10.0 + - + +
404U CYS* 2.9 41.1 + - - -
415U PHE* 4.1 20.0 - - + -
418U LEU* 4.3 10.1 - - + -
419U LEU* 4.8 1.3 - - + -
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Residues in contact with GLU 401 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397U TYR 3.0 18.2 + - - +
398U ALA* 3.8 8.5 - - - +
400U LEU* 1.3 76.0 - - - +
402U ALA* 1.3 63.8 + - - +
404U CYS* 3.3 1.6 + - - +
405U LYS* 3.0 58.4 + - + +
415U PHE* 3.6 38.3 - - + -
418X GLU* 4.0 13.3 - - - +
430X GLN* 5.7 5.0 - - - +
432X PHE* 5.7 1.0 - - - -
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Residues in contact with ALA 402 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228U GLU* 6.1 0.9 - - - +
398U ALA 3.1 18.3 + - - +
399U SER* 3.6 7.6 - - - +
401U GLU* 1.3 78.5 - - - +
403U TYR* 1.3 62.4 + - - +
405U LYS* 3.4 7.0 + - - +
406U HIS* 3.1 24.6 + - - +
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Residues in contact with TYR 403 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639B GLU* 5.7 0.7 + - - -
232U VAL* 4.2 20.0 - - + -
363U ASP* 2.7 33.3 + - - -
365U THR* 3.7 34.7 + - + -
366U GLU* 3.7 25.6 - - + -
399U SER 3.0 15.6 + - - +
400U LEU* 3.4 12.8 - - + +
402U ALA* 1.3 77.2 - - - +
404U CYS* 1.3 64.0 + - - +
406U HIS* 3.9 3.8 - - - +
407U LYS* 2.9 62.5 + - + +
408U TYR* 4.2 5.6 - + - -
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Residues in contact with CYS 404 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366U GLU* 3.7 11.2 - - - -
400U LEU* 2.9 29.4 + - - +
401U GLU* 3.8 5.6 - - - +
403U TYR* 1.3 78.2 - - - +
405U LYS* 1.3 63.4 + - + +
408U TYR* 2.9 40.9 + - - +
411U GLN 5.1 0.6 - - - +
414U ARG* 4.6 8.5 - - + -
415U PHE* 4.4 22.2 - - + +
418U LEU* 3.4 32.5 - - - -
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Residues in contact with LYS 405 (chain U).
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* 3.0 48.9 + - + +
402U ALA* 3.8 6.3 - - - +
404U CYS* 1.3 77.8 - - - +
406U HIS* 1.3 61.5 + - - +
408U TYR 4.9 2.2 - - - -
409U PRO* 3.8 19.2 - - - +
412U PRO* 3.9 31.2 + - + +
415U PHE* 4.5 11.3 - - - +
418X GLU* 4.8 9.3 + - - -
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Residues in contact with HIS 406 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ALA 4.9 8.9 + - - -
281A GLU* 3.1 40.6 + - - -
285A ARG* 5.5 6.2 + - - -
402U ALA 3.1 16.4 + - - +
403U TYR* 3.9 4.3 - - - +
404U CYS 3.2 0.2 - - - -
405U LYS* 1.3 76.5 - - - +
407U LYS* 1.3 77.4 + - + +
409U PRO* 3.3 15.4 - - - +
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Residues in contact with LYS 407 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 2.7 31.3 + - - +
639B GLU* 5.1 11.9 - - - +
403U TYR* 2.9 52.6 + - + +
406U HIS* 1.3 88.3 + - + +
408U TYR* 1.3 84.5 + - + +
409U PRO* 3.2 7.9 - - - +
410U GLU* 5.3 1.0 - - - +
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Residues in contact with TYR 408 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361U GLN 4.6 3.5 + - - -
363U ASP* 2.8 29.5 + - - +
366U GLU* 3.3 12.3 - - - -
403U TYR* 4.2 6.7 - + - -
404U CYS* 2.9 26.4 + - - +
405U LYS* 4.9 1.0 - - - -
407U LYS* 1.3 99.2 - - + +
409U PRO* 1.3 62.4 - - - +
410U GLU* 3.2 23.8 - - - -
411U GLN* 3.2 28.5 + - + +
412U PRO* 4.9 0.9 - - - +
414U ARG* 3.1 51.5 + - - -
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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