Contacts of the helix formed by residues 406 - 425 (chain A) in PDB entry 1SZU
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 GLU 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN* 4.7 10.2 - - - +
34A ARG* 3.1 37.0 + - - -
404A THR 4.8 0.9 - - - +
405A ILE* 1.3 80.2 - - - +
407A ASP* 1.3 67.2 + - - +
408A ALA* 4.2 12.8 - - + +
409A GLN* 2.9 38.2 + - + +
410A ILE* 3.1 11.3 + - - +
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Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LYS* 3.9 19.0 + - - +
405A ILE 4.0 1.4 + - - +
406A GLU* 1.3 70.0 - - - +
408A ALA* 1.3 64.7 + - - +
410A ILE* 3.1 25.2 + - - +
411A ARG* 3.3 17.9 + - + +
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A GLU* 3.1 12.4 - - + +
407A ASP* 1.3 78.8 - - - +
409A GLN* 1.3 60.8 + - + +
411A ARG* 3.1 11.8 + - - +
412A GLN* 2.8 27.0 + - - +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 4.8 1.7 - - - +
33A CYS* 3.6 16.4 - - - +
34A ARG* 3.4 44.0 - - - +
44A LEU* 3.8 27.4 - - + +
46A PHE* 4.1 1.0 - - - -
405A ILE* 3.5 16.2 - - + +
406A GLU* 2.9 49.8 + - - +
408A ALA* 1.3 73.6 - - + +
410A ILE* 1.3 65.3 + - - +
412A GLN* 4.0 21.0 + - - +
413A GLY* 3.0 19.6 + - - -
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Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 4.9 3.3 - - - -
327A LEU* 3.7 22.7 - - + -
330A LYS* 3.9 41.1 - - + +
331A LEU* 4.4 11.4 - - + -
405A ILE* 3.8 23.3 - - + +
406A GLU 3.1 10.7 + - - +
407A ASP* 3.1 21.6 + - - +
409A GLN* 1.3 76.4 - - - +
411A ARG* 1.3 69.2 + - + +
413A GLY* 3.9 0.3 - - - -
414A LEU* 3.1 42.5 + - + +
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LYS* 6.3 1.0 - - - +
407A ASP* 3.6 16.1 + - + +
408A ALA* 3.1 8.9 + - - +
410A ILE* 1.3 82.0 - - + +
412A GLN* 1.3 57.3 + - - +
414A LEU* 3.4 8.8 + - - +
415A GLU* 2.8 33.2 + - - +
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Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 5.6 3.4 + - - -
44A LEU* 3.7 25.9 - - + +
384A GLY 5.8 0.6 + - - -
408A ALA 2.8 15.6 + - - +
409A GLN* 3.8 19.0 + - - +
411A ARG* 1.3 76.8 - - - +
413A GLY* 1.3 56.6 + - - +
415A GLU* 3.4 5.3 + - - +
416A ILE* 2.9 52.3 + - + +
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.8 8.9 - - - +
46A PHE* 3.7 25.6 - - - -
385A LEU* 4.1 7.6 - - - +
409A GLN 3.0 12.1 + - - -
412A GLN* 1.3 73.4 - - - +
414A LEU* 1.3 65.9 + - - +
416A ILE* 3.4 2.0 + - - +
417A ILE* 2.9 34.1 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.9 0.6 - - + -
330A LYS 3.7 20.9 - - - +
331A LEU* 3.8 33.4 - - + +
334A GLY* 3.9 23.1 - - - +
335A LEU* 4.2 14.6 - - + -
338A ILE* 3.8 6.8 - - + +
399A ILE* 5.4 0.4 - - + -
410A ILE* 3.1 34.9 + - + +
411A ARG* 3.8 8.5 - - - +
413A GLY* 1.3 75.7 - - - +
415A GLU* 1.3 63.2 + - - +
417A ILE* 3.3 9.1 + - + +
418A SER* 2.9 24.1 + - - -
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ARG 2.8 19.7 + - - +
412A GLN* 3.6 7.2 - - - +
414A LEU* 1.3 75.2 - - - +
416A ILE* 1.3 58.1 + - + +
418A SER* 3.1 13.9 + - - -
419A GLN* 2.9 67.8 + - - +
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 5.2 1.3 - - + -
380A ALA* 4.4 0.9 - - - -
383A LYS* 3.4 49.1 - - + +
384A GLY 4.8 2.0 - - - +
385A LEU* 3.9 35.0 - - + +
412A GLN* 2.9 44.8 + - + +
413A GLY* 3.8 4.3 - - - +
415A GLU* 1.3 76.1 - - + +
417A ILE* 1.3 63.6 + - - +
419A GLN* 3.1 15.9 + - - +
420A CYS* 2.9 27.8 + - - -
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.5 6.1 - - + -
335A LEU* 4.5 14.1 - - + -
338A ILE* 3.9 13.7 - - + -
357A ILE* 5.5 1.6 - - + -
376A ILE* 5.4 4.5 - - + -
380A ALA* 5.9 0.2 - - + -
385A LEU* 3.8 19.3 - - + -
387A LEU* 4.6 16.8 - - + -
397A LEU* 6.0 1.3 - - + -
399A ILE* 4.4 22.2 - - + -
413A GLY 2.9 25.1 + - - +
414A LEU* 3.6 9.0 - - + +
415A GLU 3.2 0.2 - - - -
416A ILE* 1.3 77.0 - - - +
418A SER* 1.3 63.0 + - - +
420A CYS* 2.9 19.4 + - - +
421A PHE* 3.1 35.7 + - + -
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ILE* 3.9 30.3 - - - +
414A LEU 2.9 14.3 + - - -
415A GLU* 3.3 19.3 + - - -
417A ILE* 1.3 75.9 - - - +
419A GLN* 1.3 65.0 + - - +
421A PHE* 3.3 2.8 + - - +
422A ASP* 3.0 35.9 + - - +
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Residues in contact with GLN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 2.8 39.7 + - - +
415A GLU* 2.9 47.8 + - - +
416A ILE* 3.1 15.8 + - - +
418A SER* 1.3 75.6 - - - +
420A CYS* 1.3 52.6 + - - +
422A ASP* 3.2 7.9 + - - +
423A GLU* 2.8 47.4 + - - +
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Residues in contact with CYS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ILE* 3.7 23.3 - - + -
379A ARG* 3.5 24.0 - - + +
380A ALA* 3.4 39.9 - - - -
383A LYS* 3.8 11.4 - - - +
416A ILE* 2.9 19.5 + - - -
417A ILE* 2.9 10.5 + - - +
419A GLN* 1.3 75.7 - - - +
421A PHE* 1.3 58.2 + - - +
423A GLU* 3.4 1.5 + - - -
424A ALA* 3.0 31.0 + - - +
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Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ILE* 4.0 13.5 - - + -
342A HIS* 3.1 42.0 + + + +
344A GLU* 5.0 2.7 - - + -
345A ILE* 3.8 28.0 - - + -
357A ILE* 3.9 12.1 - - + -
359A LEU* 3.7 36.6 - - + -
372A LEU* 4.4 13.9 - - + -
376A ILE* 3.9 26.9 - - + -
397A LEU* 4.4 2.2 - - + -
417A ILE* 3.1 40.9 + - + -
418A SER 3.9 3.8 - - - +
420A CYS* 1.3 76.3 - - - +
422A ASP* 1.3 61.6 + - - +
424A ALA* 4.0 2.2 - - - +
425A LYS* 3.2 17.7 + - - +
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Residues in contact with ASP 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS* 4.1 23.4 + - - +
342A HIS* 2.6 35.9 + - - -
418A SER* 3.0 31.1 + - - +
419A GLN* 3.6 6.5 - - - +
421A PHE* 1.3 78.1 - - - +
423A GLU* 1.3 61.3 + - + +
424A ALA 3.4 0.2 + - - -
425A LYS* 3.4 8.4 + - - +
426A GLN* 3.0 25.0 + - - +
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ARG* 3.3 32.2 + - - +
383A LYS* 2.9 39.2 + - - -
419A GLN* 2.8 27.6 + - - +
420A CYS 4.2 1.6 - - - +
422A ASP* 1.3 72.1 - - + +
424A ALA* 1.3 62.3 + - - +
426A GLN* 3.5 36.1 + - - +
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 4.2 19.5 - - + +
375A GLU* 3.2 34.4 - - - +
376A ILE* 4.4 4.3 - - + -
379A ARG* 3.5 7.6 + - - +
420A CYS 3.0 17.7 + - - +
421A PHE 4.0 3.8 - - - +
423A GLU* 1.3 74.9 - - - +
425A LYS* 1.3 59.3 + - - +
426A GLN* 3.1 13.1 + - - +
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS 4.1 3.9 + - - +
342A HIS* 3.5 22.0 + - + +
343A PRO* 3.3 21.2 - - - +
344A GLU* 2.5 41.8 + - - -
421A PHE 3.2 16.7 + - - +
422A ASP 3.4 6.0 + - - +
423A GLU 3.4 0.2 - - - -
424A ALA* 1.3 75.1 - - - +
426A GLN* 1.3 64.6 + - - +
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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