Contacts of the helix formed by residues 406 - 426 (chain N) in PDB entry 2DYS
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 406 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405N LEU* 1.3 72.6 - - - +
407N ASP* 1.3 62.5 + - - +
408N THR* 3.1 12.5 + - - -
409N TRP* 2.9 46.7 + - + +
410N ALA* 3.1 19.6 + - - +
471N ILE* 4.9 5.2 + - + +
474N GLU* 3.8 22.0 + - + +
480N ARG* 3.2 9.6 - - - +
608N PGV 3.0 47.5 - - - +
15Z GLN* 5.2 2.8 + - - +
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Residues in contact with ASP 407 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333N LYS* 6.1 1.2 - - - -
335N SER* 4.9 4.5 - - - -
336N PRO* 3.6 27.6 - - + +
405N LEU* 3.3 12.4 + - - +
406N ASN* 1.3 72.8 + - - +
408N THR* 1.3 62.0 - - - +
410N ALA* 3.4 4.7 + - - +
411N LYS* 3.0 39.3 + - - +
608N PGV 5.7 5.9 + - - +
77Q GLU* 4.5 2.9 - - - +
1Z ILE* 6.2 0.2 - - - +
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Residues in contact with THR 408 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ASN* 3.1 8.1 + - - -
407N ASP* 1.3 74.0 - - - +
409N TRP* 1.3 66.5 + - - +
411N LYS* 3.1 5.4 + - - +
412N ILE* 3.0 29.9 + - + +
608N PGV 3.1 38.7 + - + -
77Q GLU* 2.9 19.1 + - - +
80Q THR* 4.2 9.6 - - + -
81Q VAL* 3.6 22.0 - - + -
10X HIS* 3.7 19.4 + - + -
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Residues in contact with TRP 409 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ASN* 2.9 43.2 + - + +
408N THR* 1.3 75.2 - - - +
410N ALA* 1.3 57.3 + - - +
412N ILE* 3.1 22.6 + - + +
413N HIS 2.9 24.4 + - - -
467N LEU* 4.0 19.2 - - + +
470N PHE* 3.8 26.6 - + - -
471N ILE* 3.5 23.2 - - + +
474N GLU* 5.2 5.4 - - + -
608N PGV 3.4 53.4 - - + +
88Q PHE* 3.6 35.7 - + - -
15Z GLN* 3.1 26.2 + - - -
19Z LEU* 4.4 8.7 - - + -
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Residues in contact with ALA 410 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336N PRO* 3.6 25.6 - - + +
340N TRP* 4.8 2.7 + - - +
394N VAL* 5.1 12.3 - - + -
405N LEU* 5.4 8.1 - - + -
406N ASN 3.1 11.9 + - - +
407N ASP* 3.5 10.1 - - - +
409N TRP* 1.3 76.8 - - - +
411N LYS* 1.3 57.3 + - - +
413N HIS* 3.4 11.8 + - - +
414N PHE* 3.0 27.0 + - - +
471N ILE* 4.1 10.4 - - + +
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Residues in contact with LYS 411 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334N TRP 3.3 24.8 + - - -
335N SER* 4.8 0.4 - - - +
336N PRO* 3.9 20.9 - - + -
339N MET* 4.0 17.7 - - + -
407N ASP* 3.0 26.0 + - - +
408N THR 3.1 6.7 + - - +
410N ALA* 1.3 74.3 - - - +
412N ILE* 1.3 66.0 + - - +
414N PHE* 3.4 10.2 + - - +
415N ALA* 3.1 22.3 + - - +
607N TGL 3.5 31.2 + - + +
77Q GLU* 3.1 39.1 + - - +
81Q VAL* 3.9 16.7 - - + +
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Residues in contact with ILE 412 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408N THR* 3.0 24.6 + - + +
409N TRP* 3.3 27.4 - - + +
411N LYS* 1.3 74.6 - - - +
413N HIS* 1.3 65.4 + - - +
415N ALA* 3.2 6.1 + - - +
416N ILE* 3.0 45.4 + - + +
467N LEU* 4.0 8.7 - - + -
608N PGV 3.9 16.6 - - + -
80Q THR 4.5 0.7 - - - +
81Q VAL* 3.7 28.0 - - - +
84Q ALA* 3.5 30.1 - - + -
85Q ALA 4.0 7.2 - - - +
88Q PHE* 4.2 4.9 - - + -
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Residues in contact with HIS 413 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340N TRP* 3.3 33.9 + + - -
390N MET* 3.5 28.3 - - + +
394N VAL* 5.8 2.0 - - - +
409N TRP 2.9 12.8 + - - +
410N ALA* 3.5 10.5 + - - +
412N ILE* 1.3 76.6 - - - +
414N PHE* 1.3 63.6 + - - +
416N ILE* 3.2 4.4 + - - +
417N MET* 3.0 36.5 + - - +
464N ALA* 3.2 33.8 + - + -
465N VAL* 5.2 0.2 - - - -
467N LEU* 4.1 10.5 - - + +
468N MET* 3.7 18.6 - - + +
471N ILE* 3.8 14.7 - - + +
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Residues in contact with PHE 414 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336N PRO* 5.3 1.1 - - + +
339N MET* 3.4 44.9 - - + -
340N TRP* 3.6 47.1 - + + +
343N GLY* 4.9 0.2 - - - -
387N PHE* 4.2 17.7 - + - -
410N ALA 3.0 14.4 + - - +
411N LYS* 3.5 10.1 - - - +
412N ILE 3.3 0.2 - - - -
413N HIS* 1.3 78.0 + - - +
415N ALA* 1.3 59.2 + - - +
417N MET* 3.3 2.1 + - - +
418N PHE* 2.9 48.2 + + - +
607N TGL 3.4 54.3 - - + -
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Residues in contact with ALA 415 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411N LYS 3.1 10.3 + - - +
412N ILE* 3.2 8.9 + - - +
414N PHE* 1.3 84.8 - - - +
416N ILE* 1.3 62.4 + - - +
418N PHE* 3.4 2.2 + - - +
419N VAL* 3.2 30.3 + - - +
607N TGL 3.8 36.6 - - + +
81Q VAL* 4.8 4.7 - - + -
85Q ALA* 4.0 17.0 - - + -
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Residues in contact with ILE 416 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412N ILE* 3.0 23.8 + - + +
413N HIS* 3.7 5.2 - - - +
415N ALA* 1.3 74.6 - - - +
417N MET* 1.3 58.3 + - - +
419N VAL* 3.3 6.2 + - - +
420N GLY 2.9 24.3 + - - -
460N ILE* 3.4 41.3 - - + +
463N THR* 4.5 7.4 - - + -
464N ALA* 3.8 14.1 - - + +
467N LEU* 3.6 28.5 - - + -
85Q ALA* 4.0 20.4 - - - +
88Q PHE* 3.6 23.8 - - + -
89Q ILE* 4.6 9.2 - - + +
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Residues in contact with MET 417 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340N TRP* 3.7 25.8 - - + -
386N VAL* 5.4 5.6 - - + -
387N PHE* 4.2 10.3 - - + -
390N MET* 5.6 3.1 - - + -
413N HIS* 3.0 30.6 + - + +
414N PHE 3.6 3.6 - - - +
416N ILE* 1.3 73.9 - - - +
418N PHE* 1.3 61.4 + - - +
420N GLY* 4.8 1.6 - - - -
421N VAL* 2.9 44.4 + - + +
461N SER* 4.1 19.7 - - - +
464N ALA* 3.7 24.4 - - + +
465N VAL* 4.1 20.9 - - + -
468N MET* 6.5 0.9 - - - -
604N HEA 4.9 19.7 - - + -
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Residues in contact with PHE 418 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343N GLY* 4.6 2.0 - - - -
346N PHE* 5.2 4.5 - + - -
347N LEU* 4.1 22.4 - - + -
387N PHE* 4.2 14.3 - + - -
414N PHE* 2.9 38.2 + + + +
415N ALA 3.5 6.3 - - - +
416N ILE 3.3 0.2 - - - -
417N MET* 1.3 77.7 - - - +
419N VAL* 1.3 66.8 + - + +
421N VAL* 3.5 5.3 - - - +
422N ASN* 2.7 49.2 + - + +
607N TGL 3.8 58.6 - - + -
303O TGL 5.8 9.9 - - + -
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Residues in contact with VAL 419 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415N ALA 3.2 16.9 + - - +
416N ILE 3.5 6.1 - - - +
418N PHE* 1.3 78.3 - - + +
420N GLY* 1.3 66.3 + - - +
422N ASN* 3.3 3.4 + - - +
423N MET* 2.9 37.1 + - + +
460N ILE* 4.1 16.4 - - + -
607N TGL 4.3 32.8 - - + -
89Q ILE* 3.8 29.2 - - + -
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Residues in contact with GLY 420 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416N ILE 2.9 11.4 + - - -
417N MET 3.2 3.1 + - - -
419N VAL* 1.3 78.2 - - - +
421N VAL* 1.3 57.1 + - - +
423N MET* 3.2 0.7 + - - +
424N THR* 2.8 31.2 + - - -
457N GLY* 3.3 18.4 - - - +
460N ILE* 3.5 16.3 - - - +
461N SER* 3.4 11.7 - - - -
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Residues in contact with VAL 421 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382N SER* 3.9 26.7 - - - +
383N MET* 3.3 28.6 - - + +
387N PHE* 4.1 8.7 - - + -
417N MET* 2.9 37.4 + - + +
418N PHE* 3.5 10.3 - - - +
420N GLY* 1.3 71.3 - - - +
422N ASN* 1.3 65.4 + - - +
424N THR* 4.2 3.6 - - - -
425N PHE* 3.0 37.0 + - + -
461N SER* 3.4 13.4 + - - +
604N HEA 4.1 7.0 - - + +
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Residues in contact with ASN 422 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347N LEU* 3.7 17.0 - - - +
379N TYR* 3.5 9.7 + - - -
383N MET* 3.8 7.9 - - - +
418N PHE* 2.7 50.4 + - + +
419N VAL* 3.3 3.5 + - - +
420N GLY 3.3 0.4 - - - -
421N VAL* 1.3 82.6 - - - +
423N MET* 1.3 61.6 + - - +
426N PHE* 2.9 35.6 + - - +
303O TGL 3.3 44.9 - - + +
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Residues in contact with MET 423 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419N VAL* 2.9 27.1 + - + +
420N GLY* 3.6 4.3 - - - +
422N ASN* 1.3 77.1 - - - +
424N THR* 1.3 62.2 + - - +
427N PRO* 3.2 20.4 - - - +
453N ILE* 3.7 23.2 - - + +
454N SER* 3.6 6.8 - - - -
456N MET* 4.2 8.1 - - - +
457N GLY* 3.4 25.6 - - - -
460N ILE* 3.7 20.6 - - + -
303O TGL 5.2 10.3 - - + -
29X TRP* 4.6 11.4 - - + -
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Residues in contact with THR 424 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ARG* 4.1 5.2 - - - -
420N GLY 2.8 21.5 + - - -
421N VAL* 3.7 5.0 - - - -
422N ASN 3.2 0.2 - - - -
423N MET* 1.3 78.8 - - - +
425N PHE* 1.3 89.2 + - + +
427N PRO* 3.8 2.4 - - - +
428N GLN* 3.6 5.2 + - - +
454N SER* 2.7 50.6 + - - +
457N GLY 2.8 1.2 + - - -
458N SER* 2.8 22.0 + - - -
461N SER* 4.2 1.7 + - - -
604N HEA 4.0 16.3 + - + +
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Residues in contact with PHE 425 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374N VAL 4.8 0.2 - - - -
375N ALA* 4.0 6.0 - - - +
378N HIS* 3.2 43.1 - + + -
379N TYR* 3.8 21.3 - - + -
382N SER* 3.6 12.1 - - - -
383N MET* 3.7 10.8 - - + -
421N VAL* 3.0 29.8 + - + +
424N THR* 1.3 90.2 - - + +
426N PHE* 1.3 67.4 + - - +
427N PRO 3.4 2.2 - - - -
428N GLN* 3.1 40.2 + - - +
429N HIS* 3.8 5.5 + - - -
604N HEA 3.3 53.2 - + + -
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Residues in contact with PHE 426 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379N TYR* 3.4 23.1 + + - +
422N ASN 2.9 19.4 + - - +
425N PHE* 1.3 73.9 - - - +
427N PRO* 1.3 69.2 - - + +
428N GLN 3.1 0.2 + - - -
429N HIS* 2.7 43.9 + + - +
430N PHE* 3.8 26.5 + + - -
303O TGL 3.5 124.3 - - + -
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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