Contacts of the helix formed by residues 424 - 438 (chain A) in PDB entry 1ASZ
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 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A HIS* 5.2 2.9 - - - +
333A ARG* 3.3 31.1 + - - +
422A LEU 3.9 0.8 + - - -
423A SER* 1.3 69.8 - - - +
425A GLU* 1.3 64.8 + - - +
427A GLU* 3.3 11.1 + - - +
428A LYS* 3.1 48.6 + - - +
477A GLU* 4.6 0.2 - - - +
672R A 4.0 15.9 - - - +
673R G 2.3 44.7 + - - +
674R C 5.7 0.7 + - - -
675R C 5.5 2.3 + - - -
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Residues in contact with GLU 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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414A LYS* 3.6 25.8 + - - +
423A SER* 2.9 10.4 + - - +
424A THR* 1.3 80.6 - - - +
426A ASN* 1.3 67.9 - - - +
428A LYS* 3.1 7.1 + - - +
429A PHE* 3.1 20.6 + - + +
672R A 4.4 17.8 + - - +
673R G 4.5 0.6 + - - -
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Residues in contact with ASN 426 (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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409A LEU* 3.7 25.8 - - + +
414A LYS* 3.4 43.5 - - - +
416A ILE* 5.1 7.5 - - - +
420A GLU* 5.5 2.4 - - - +
422A LEU* 4.3 9.9 - - + -
423A SER* 2.8 24.7 + - - +
425A GLU* 1.3 82.3 + - - +
427A GLU* 1.3 57.7 + - - +
429A PHE* 3.1 3.1 + - - +
430A LEU* 2.8 34.3 + - - +
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Residues in contact with GLU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 2.6 36.9 + - - -
422A LEU* 4.3 28.1 - - + +
423A SER 2.9 10.2 + - - +
424A THR* 3.4 14.2 - - - +
425A GLU 3.2 0.2 - - - -
426A ASN* 1.3 77.1 - - - +
428A LYS* 1.3 61.7 + - + +
430A LEU* 3.8 3.0 + - - +
431A GLY* 3.3 14.2 + - - -
443A TYR* 4.8 4.2 + - - -
473A PHE* 3.6 23.6 - - + -
476A GLY 3.2 12.2 - - - +
477A GLU* 3.4 1.7 - - - -
478A GLU* 3.1 25.6 + - - +
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Residues in contact with LYS 428 (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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332A HIS* 4.4 9.4 + - - -
333A ARG* 5.5 0.4 - - - +
424A THR* 3.1 29.2 + - + +
425A GLU* 3.6 7.4 - - - +
427A GLU* 1.3 76.9 - - + +
429A PHE* 1.3 59.8 + - - +
431A GLY* 3.0 4.3 + - - -
432A LYS* 2.8 26.9 + - - +
476A GLY* 3.6 16.4 - - - +
477A GLU* 3.5 30.1 - - + +
671R G 5.4 4.8 + - - -
672R A 3.4 28.3 + - - +
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Residues in contact with PHE 429 (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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409A LEU* 4.3 5.2 - - + -
412A ALA* 4.4 15.9 - - + -
414A LYS* 3.2 48.2 - - + -
425A GLU* 3.1 14.5 + - + +
426A ASN* 3.6 10.5 - - - +
428A LYS* 1.3 72.2 - - - +
430A LEU* 1.3 57.8 + - - +
431A GLY 2.9 1.3 - - - -
432A LYS* 2.5 63.2 + - + +
433A LEU* 2.8 44.1 + - + +
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Residues in contact with LEU 430 (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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400A LEU* 5.1 1.6 - - + -
405A GLY* 4.1 31.2 - - - +
408A MET* 4.0 25.4 - - + -
409A LEU* 3.8 18.0 - - + +
422A LEU* 4.1 23.3 - - + -
426A ASN 2.8 19.4 + - - +
427A GLU 4.1 3.8 - - - +
429A PHE* 1.3 71.6 - - - +
431A GLY* 1.3 49.8 + - - +
433A LEU* 3.2 7.0 + - + +
434A VAL* 2.7 54.9 + - + +
443A TYR* 3.5 21.1 - - + +
445A LEU* 4.7 10.1 - - + -
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Residues in contact with GLY 431 (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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427A GLU 3.3 10.1 + - - -
428A LYS 3.0 8.2 + - - -
429A PHE 2.9 1.2 - - - -
430A LEU* 1.3 77.4 - - - +
432A LYS* 1.3 64.5 + - - +
434A VAL* 3.3 8.8 + - - +
435A ARG* 3.0 22.7 + - - +
440A THR 5.1 0.7 - - - +
443A TYR* 4.7 9.4 - - - -
476A GLY* 4.0 20.0 - - - -
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Residues in contact with LYS 432 (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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428A LYS* 2.8 8.5 + - - +
429A PHE* 2.5 51.6 + - + +
431A GLY* 1.3 68.9 - - - +
433A LEU* 1.3 53.1 + - - +
435A ARG* 2.8 29.4 + - - +
436A ASP* 3.1 25.1 + - - +
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Residues in contact with LEU 433 (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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408A MET* 3.9 43.5 - - + +
409A LEU* 4.0 23.6 - - + -
412A ALA* 4.7 8.5 - - + -
429A PHE* 2.8 50.4 + - + +
430A LEU* 3.4 10.5 - - + +
432A LYS* 1.3 72.1 - - - +
434A VAL* 1.3 58.7 + - - +
436A ASP* 3.0 15.6 + - + +
437A LYS* 2.9 30.1 + - - +
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Residues in contact with VAL 434 (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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398A VAL* 4.9 1.1 - - + -
400A LEU* 4.3 8.3 - - + -
408A MET* 4.8 1.8 - - + -
430A LEU* 2.7 48.7 + - + +
431A GLY* 4.2 4.0 - - - +
432A LYS 3.3 0.4 - - - -
433A LEU* 1.3 73.2 - - - +
435A ARG* 1.3 62.6 + - - +
438A TYR* 3.1 40.3 + - + +
439A ASP 3.7 1.2 + - - -
440A THR* 4.0 18.8 + - + +
443A TYR* 3.8 44.6 - - + -
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Residues in contact with ARG 435 (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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387A GLU* 3.1 37.2 + - - +
388A GLU 4.7 0.2 + - - -
390A LYS* 3.0 55.3 + - + +
431A GLY 3.0 10.7 + - - +
432A LYS* 2.8 13.9 + - - +
434A VAL* 1.3 77.9 - - - +
436A ASP* 1.3 61.9 + - - +
439A ASP* 2.7 34.0 + - - +
440A THR 3.4 19.5 - - - +
441A ASP* 3.6 25.4 + - - +
475A ARG* 6.0 0.4 - - - +
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Residues in contact with ASP 436 (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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432A LYS* 3.1 28.9 + - - +
433A LEU* 3.0 15.0 + - + +
435A ARG* 1.3 87.0 - - - +
437A LYS* 1.3 70.0 + - - +
439A ASP* 3.4 6.1 + - - +
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Residues in contact with LYS 437 (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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408A MET* 4.1 13.2 - - + -
433A LEU 2.9 17.1 + - - +
436A ASP* 1.3 76.5 - - - +
438A TYR* 1.3 92.9 + - + +
439A ASP* 5.0 0.7 - - - +
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Residues in contact with TYR 438 (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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392A PRO* 3.9 15.4 - - - +
398A VAL* 3.5 33.4 - - + -
400A LEU* 3.9 30.0 - - + +
404A GLU* 5.3 2.3 + - - -
408A MET* 3.8 19.8 - - + +
434A VAL* 3.1 23.6 + - + +
437A LYS* 1.3 101.9 - - + +
439A ASP* 1.3 72.4 + - - +
440A THR* 3.3 4.8 + - + -
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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
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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