Contacts of the helix formed by residues 396 - 420 (chain Q) in PDB entry 5LN3
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 THR 396 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393Q VAL* 3.6 26.0 - - + +
395Q LYS* 1.4 88.2 - - + +
397Q TYR* 1.4 59.8 + - - +
398Q GLU 3.3 0.7 - - - -
399Q ALA 3.7 0.7 - - - -
400Q ALA* 2.9 29.6 + - - +
366R TYR* 4.3 12.1 + - - -
259U VAL* 4.4 21.3 - - + +
255V TYR* 3.0 41.7 + - + -
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Residues in contact with TYR 397 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393Q VAL* 4.8 10.1 - - + +
394Q ASP* 5.7 4.0 - - - -
395Q LYS 5.5 0.4 - - - +
396Q THR* 1.4 76.9 + - - +
398Q GLU* 1.4 65.5 - - + +
400Q ALA* 3.3 4.6 + - - +
401Q LEU* 2.8 69.4 + - + +
365R GLN* 3.4 58.6 - - + +
366R TYR* 5.4 8.3 - - + -
368R GLU* 3.2 34.7 + - + +
369R THR* 3.3 20.6 - - - -
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Residues in contact with GLU 398 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394Q ASP* 4.1 24.2 - - + +
395Q LYS* 4.2 3.0 - - - +
396Q THR 3.9 1.2 - - - +
397Q TYR* 1.4 85.0 - - + +
399Q ALA* 1.3 64.8 + - - +
401Q LEU* 3.5 18.7 + - - +
402Q GLU* 3.3 55.8 + - - +
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Residues in contact with ALA 399 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395Q LYS* 3.0 24.7 + - - +
396Q THR 3.7 0.2 - - - +
397Q TYR 3.4 0.2 - - - -
398Q GLU* 1.3 81.5 - - - +
400Q ALA* 1.3 60.7 + - - +
402Q GLU* 3.5 7.7 + - - +
403Q THR* 3.4 21.7 + - - +
255V TYR* 3.7 13.7 - - + +
259V VAL* 3.5 36.5 - - + +
263V ASP* 5.1 1.9 - - - +
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Residues in contact with ALA 400 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396Q THR 2.9 19.6 + - - +
397Q TYR* 3.3 4.7 + - - +
399Q ALA* 1.3 72.1 - - - +
401Q LEU* 1.4 65.0 + - - +
403Q THR* 3.2 25.5 + - - +
404Q ILE* 3.5 15.1 + - - +
369R THR* 3.7 24.9 - - + +
262U LEU* 4.7 10.3 - - + -
266U ILE* 4.5 11.4 - - + -
255V TYR* 4.2 4.9 + - - +
259V VAL* 6.0 0.2 - - - -
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Residues in contact with LEU 401 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397Q TYR* 2.8 55.3 + - + +
398Q GLU* 3.6 20.4 - - - +
400Q ALA* 1.4 74.0 - - - +
402Q GLU* 1.4 62.4 + - + +
404Q ILE* 3.1 31.0 - - + +
405Q GLN* 3.3 35.5 + - - +
368R GLU* 6.0 2.5 - - + +
369R THR* 4.9 4.9 - - - +
372R LYS* 5.6 6.1 - - + -
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Residues in contact with GLU 402 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398Q GLU* 3.3 42.9 + - - +
399Q ALA* 4.0 6.3 - - - +
401Q LEU* 1.4 80.8 - - + +
403Q THR* 1.4 64.9 + - - +
404Q ILE 3.4 0.7 + - - -
405Q GLN* 3.4 15.9 + - - +
406Q ASN* 3.0 22.9 + - - +
263V ASP* 4.0 25.7 - - - +
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Residues in contact with THR 403 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399Q ALA 3.4 11.9 + - - +
400Q ALA* 3.2 17.3 - - - +
402Q GLU* 1.4 81.1 - - - +
404Q ILE* 1.4 60.1 + - - +
406Q ASN* 3.7 9.2 + - - +
407Q MET* 3.3 22.3 + - - +
266U ILE* 3.7 34.0 - - + +
259V VAL* 6.0 5.8 - - + -
262V GLU* 3.2 31.3 + - - +
263V ASP* 4.5 9.6 - - - +
266V THR* 5.8 1.2 - - - +
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Residues in contact with ILE 404 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400Q ALA 3.5 13.5 - - - +
401Q LEU* 3.1 32.8 - - + +
403Q THR* 1.4 72.5 - - + +
405Q GLN* 1.4 57.4 + - + +
407Q MET* 3.2 7.8 + - - +
408Q SER* 2.9 33.4 + - - -
369R THR* 3.8 33.9 - - + +
372R LYS* 3.8 24.7 - - + +
373R GLY* 5.2 7.9 - - - +
376R LEU* 4.1 13.8 - - + +
266U ILE* 4.2 26.7 - - + -
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Residues in contact with GLN 405 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401Q LEU* 3.3 43.3 - - + +
402Q GLU* 3.4 9.6 + - - +
404Q ILE* 1.4 77.6 - - + +
406Q ASN* 1.4 61.5 + - - +
408Q SER* 3.5 5.5 + - - -
409Q LYS* 3.4 16.6 + - - +
372R LYS* 4.2 25.6 - - + +
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Residues in contact with ASN 406 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402Q GLU* 3.0 28.1 + - - +
403Q THR* 3.8 8.4 - - - +
405Q GLN* 1.4 76.8 - - - +
407Q MET* 1.4 59.3 + - - +
409Q LYS* 3.1 28.3 + - - +
410Q VAL* 3.2 19.9 + - + +
263V ASP* 4.5 16.7 + - - +
266V THR* 3.7 28.3 + - + +
267V PRO* 5.5 2.8 - - - +
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Residues in contact with MET 407 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403Q THR 3.3 14.7 + - - +
404Q ILE* 3.2 8.6 + - - +
406Q ASN* 1.4 76.3 - - - +
408Q SER* 1.4 58.4 + - - +
410Q VAL* 3.3 8.7 + - - +
411Q VAL* 3.0 52.2 + - + +
376R LEU* 3.8 17.0 - - + -
380R VAL* 5.8 0.4 - - + -
266U ILE* 5.7 5.2 - - + -
269U VAL* 3.5 48.0 - - + +
270U VAL* 3.8 27.4 - - + +
273U HIS* 4.1 18.4 - - + -
266V THR* 5.3 9.6 - - + -
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Residues in contact with SER 408 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404Q ILE 2.9 14.5 + - - -
405Q GLN* 3.6 11.7 - - - -
406Q ASN 3.3 0.2 - - - -
407Q MET* 1.4 72.3 - - - +
409Q LYS* 1.4 64.0 + - - -
411Q VAL* 3.4 2.8 + - - +
412Q ASP* 3.2 21.3 + - - +
372R LYS* 4.3 17.4 + - - -
376R LEU* 3.4 31.4 - - - +
379R ARG* 5.8 4.4 - - - +
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Residues in contact with LYS 409 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405Q GLN 3.4 8.5 + - - +
406Q ASN* 3.1 20.0 + - - +
408Q SER* 1.4 76.5 - - - +
410Q VAL* 1.4 59.6 + - + +
412Q ASP* 3.2 15.4 + - - +
413Q SER* 2.8 28.4 + - - +
267V PRO* 5.9 4.2 - - - +
270V LEU* 4.1 26.3 - - - +
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Residues in contact with VAL 410 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406Q ASN* 3.2 17.7 + - + +
407Q MET* 3.7 11.7 - - - +
409Q LYS* 1.4 75.5 - - + +
411Q VAL* 1.4 66.6 + - - +
413Q SER* 3.3 8.6 + - - -
414Q LEU* 3.2 21.5 + - + +
273U HIS* 3.7 14.8 - - + +
266V THR* 3.9 33.2 - - + +
267V PRO* 5.5 0.9 - - + -
269V GLN* 3.6 24.9 - - + +
270V LEU* 4.8 19.1 - - + +
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Residues in contact with VAL 411 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407Q MET* 3.0 47.0 + - + +
408Q SER 3.9 4.3 - - - +
410Q VAL* 1.4 76.3 - - - +
412Q ASP* 1.4 62.9 + - - +
414Q LEU* 3.1 14.0 + - - +
415Q TYR* 3.3 11.8 + - + +
376R LEU* 4.2 11.4 - - + -
379R ARG* 4.1 29.2 - - + +
380R VAL* 4.9 7.4 - - + +
383R LEU* 4.2 21.3 - - + +
273U HIS* 3.6 16.2 - - + +
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Residues in contact with ASP 412 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408Q SER 3.2 9.1 + - - +
409Q LYS* 3.2 12.8 + - - +
411Q VAL* 1.4 76.2 - - - +
413Q SER* 1.4 64.5 + - - +
415Q TYR* 3.3 17.6 + - - +
416Q ASN* 3.1 20.7 - - - +
379R ARG* 4.2 13.6 - - - +
382R LYS* 4.1 17.7 + - - +
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Residues in contact with SER 413 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409Q LYS* 2.8 20.1 + - - +
410Q VAL* 3.6 8.4 - - - -
412Q ASP* 1.4 60.6 - - - +
414Q LEU* 1.3 64.2 + - - +
416Q ASN* 3.0 21.7 + - - +
417Q LYS* 3.4 28.0 + - - +
270V LEU* 4.0 26.0 - - - +
273V LYS* 6.0 2.9 - - - -
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Residues in contact with LEU 414 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410Q VAL 3.2 5.6 + - - +
411Q VAL 3.1 11.3 + - - +
413Q SER* 1.3 80.6 - - - +
415Q TYR* 1.3 61.0 + - - +
417Q LYS* 3.5 8.8 + - + +
418Q ALA* 3.0 21.3 + - + +
383R LEU* 4.7 5.6 - - + -
273U HIS* 3.2 46.9 - - + +
276U ILE* 4.2 17.5 - - + -
277U ASN* 3.5 27.1 - - + +
280U ILE* 4.3 17.5 - - + -
269V GLN* 5.8 2.7 - - - +
273V LYS* 4.0 20.9 - - + -
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Residues in contact with TYR 415 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411Q VAL* 3.3 8.3 + - + +
412Q ASP* 3.3 13.6 + - - +
413Q SER 3.2 0.2 - - - -
414Q LEU* 1.3 78.1 - - - +
416Q ASN* 1.3 73.4 + - - +
418Q ALA* 3.2 2.8 + - - +
419Q LYS* 3.0 56.6 + - + +
382R LYS* 3.8 49.8 - - + +
383R LEU* 4.0 34.1 - - + +
386R VAL* 3.5 38.8 - - + +
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Residues in contact with ASN 416 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412Q ASP* 3.1 25.1 - - - +
413Q SER* 3.0 11.7 + - - +
415Q TYR* 1.3 87.2 - - - +
417Q LYS* 1.4 62.4 + - - +
419Q LYS* 3.4 14.5 + - - +
420Q LYS 3.8 3.3 + - - -
421Q LEU 3.7 11.5 + - - +
422Q THR* 3.4 51.7 + - + +
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Residues in contact with LYS 417 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413Q SER* 3.7 30.6 + - - +
414Q LEU* 3.8 9.9 - - + +
416Q ASN* 1.4 80.0 - - - +
418Q ALA* 1.3 65.9 + - - +
419Q LYS 3.4 0.2 + - - -
420Q LYS* 3.9 8.7 + - - +
422Q THR* 4.3 15.7 + - - +
270V LEU* 5.7 3.6 - - - +
273V LYS* 3.9 37.1 - - + +
274V ASN* 4.4 21.2 - - - +
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Residues in contact with ALA 418 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414Q LEU* 3.0 19.3 + - - +
415Q TYR* 3.4 8.5 - - - +
417Q LYS* 1.3 78.0 - - - +
419Q LYS* 1.4 66.2 + - - +
420Q LYS* 3.5 13.5 + - - +
383R LEU* 4.6 8.7 - - + -
386R VAL* 5.5 4.9 - - + -
387R ILE* 5.1 12.7 - - + +
280U ILE* 4.0 36.9 - - + +
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Residues in contact with LYS 419 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415Q TYR* 3.0 46.3 + - + +
416Q ASN* 3.4 9.2 - - - +
417Q LYS 3.2 0.4 - - - -
418Q ALA* 1.4 81.6 - - - +
420Q LYS* 1.4 71.7 + - - +
421Q LEU* 3.6 41.8 - - + +
386R VAL* 5.5 12.8 - - + -
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Residues in contact with LYS 420 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416Q ASN 3.8 2.8 + - - -
417Q LYS 3.9 6.2 + - - +
418Q ALA 3.5 11.7 + - - +
419Q LYS* 1.4 79.9 + - - +
421Q LEU* 1.3 69.5 + - - +
387R ILE* 6.3 0.8 - - - +
284U ASP* 5.3 9.0 + - - -
287U LYS* 5.4 15.7 - - - +
288U LYS* 5.4 9.2 - - - +
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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