Contacts of the helix formed by residues 428 - 438 (chain A) in PDB entry 2ADU
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 TYR 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A LEU* 3.6 18.3 - - + +
417A ARG* 3.2 34.5 + - + +
420A LEU* 3.8 30.5 - - + -
421A ASP* 2.7 30.0 + - - -
425A GLU* 3.6 38.8 - - + +
426A SER* 3.7 6.7 - - - +
427A LYS* 1.3 77.7 - - - +
429A LEU* 1.3 86.3 + - + +
430A MET 3.3 2.5 - - - -
431A ALA* 3.2 10.3 + - + +
432A LEU* 2.8 35.3 + - + +
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Residues in contact with LEU 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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383A TYR* 5.7 0.4 - - - +
417A ARG* 3.6 40.6 - - + +
427A LYS* 3.8 1.0 - - - +
428A TYR* 1.3 102.1 - - + +
430A MET* 1.3 58.7 + - - +
432A LEU* 3.2 10.7 + - + +
433A LYS* 2.9 28.6 + - - +
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Residues in contact with MET 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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398A ARG* 5.9 5.8 - - - +
427A LYS 5.5 0.2 - - - -
428A TYR 3.3 0.8 - - - +
429A LEU* 1.3 75.7 - - - +
431A ALA* 1.3 66.7 + - - +
433A LYS* 3.1 25.8 + - + +
434A ASN* 2.9 40.4 + - - +
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Residues in contact with ALA 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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398A ARG* 3.6 35.0 - - + +
399A THR* 3.7 18.8 - - - +
402A LEU* 3.6 13.5 - - + -
427A LYS 5.3 0.4 - - - +
428A TYR* 3.2 16.2 + - - +
430A MET* 1.3 77.0 - - - +
432A LEU* 1.3 62.9 + - - +
434A ASN* 3.2 6.1 + - - +
435A LEU* 3.1 24.8 + - - +
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR* 3.6 55.9 - - + +
402A LEU* 3.3 15.8 - - + +
406A ILE* 4.7 0.4 - - + -
415A PHE* 4.5 11.9 - - + -
417A ARG* 4.8 3.1 - - + -
420A LEU* 4.6 17.3 - - + -
428A TYR* 2.8 27.7 + - + +
429A LEU* 3.4 10.5 - - + +
431A ALA* 1.3 77.2 - - - +
433A LYS* 1.3 60.7 + - - +
435A LEU* 3.2 11.3 + - + +
436A CYS* 3.0 26.6 + - - -
441A VAL* 4.1 14.8 - - + -
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Residues in contact with LYS 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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429A LEU 2.9 13.6 + - - +
430A MET* 3.1 29.4 + - + +
432A LEU* 1.3 76.4 - - - +
434A ASN* 1.3 54.4 + - - +
436A CYS* 3.2 8.5 + - + +
437A ASP* 2.8 63.1 + - - +
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Residues in contact with ASN 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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396A LEU* 4.4 14.0 - - + +
399A THR* 2.8 31.3 + - + +
430A MET* 2.9 33.4 + - - +
431A ALA* 3.2 8.3 + - - +
433A LYS* 1.3 77.3 - - - +
435A LEU* 1.3 52.7 + - - +
437A ASP* 3.0 11.6 + - - +
438A LEU* 2.7 46.0 + - + +
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Residues in contact with LEU 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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394A ILE* 5.4 0.7 - - + -
399A THR* 3.8 19.5 - - + -
402A LEU* 3.8 32.8 - - + -
403A LEU* 3.9 26.9 - - + +
406A ILE* 3.8 22.4 - - + -
431A ALA 3.1 8.0 + - - +
432A LEU* 3.5 7.9 - - + +
434A ASN* 1.3 80.3 - - - +
436A CYS* 1.3 59.4 + - - +
438A LEU* 3.3 5.5 + - + +
439A GLY 3.1 2.9 + - - -
440A ILE* 3.0 52.4 + - + +
441A VAL* 3.1 18.6 + - + +
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Residues in contact with CYS 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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383A TYR* 3.9 20.0 - - - -
432A LEU 3.0 19.4 + - - -
433A LYS* 3.5 11.2 - - + +
435A LEU* 1.3 77.6 - - - +
437A ASP* 1.3 59.8 + - - +
439A GLY* 2.9 19.4 + - - -
441A VAL* 3.0 37.0 - - - +
442A ASP* 5.4 0.5 - - - +
443A PRO* 3.9 23.7 - - + +
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Residues in contact with ASP 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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433A LYS* 2.8 57.9 + - - +
434A ASN* 3.5 10.0 - - - +
436A CYS* 1.3 74.4 - - - +
438A LEU* 1.3 60.9 + - + +
439A GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 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 VAL* 5.5 3.6 - - + -
394A ILE* 4.0 20.6 - - + -
396A LEU* 6.1 3.6 - - + -
399A THR* 4.7 5.8 - - + -
434A ASN* 2.7 34.8 + - + +
435A LEU* 3.6 7.0 - - - +
436A CYS 3.1 0.2 - - - -
437A ASP* 1.3 73.8 - - + +
439A GLY* 1.3 60.5 + - - +
440A ILE* 3.5 28.7 + - + +
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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