Contacts of the helix formed by residues 424 - 441 (chain A) in PDB entry 1AX4
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 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.5 32.6 + - + +
5A ILE 3.0 33.7 + - - +
7A GLU* 4.5 3.4 + - - -
327A TYR* 4.8 4.6 - - - -
331A GLN* 3.3 34.6 + - - +
334A TYR* 3.8 8.0 - - + -
423A THR* 1.3 73.4 - - - +
425A ASP* 1.3 57.4 + - - +
427A MET* 3.2 9.9 + - - +
428A ASP* 2.8 24.1 + - - -
425C ASP* 2.7 28.2 + - - +
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Residues in contact with ASP 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 2.6 28.5 + - - +
423A THR* 3.1 10.2 + - - +
424A ASN* 1.3 76.9 - - - +
426A HIS* 1.4 59.6 + - - +
428A ASP* 3.8 7.0 - - + +
429A TYR* 3.1 25.1 + - - +
4C ARG* 2.9 20.4 + - - +
5C ILE 3.9 2.4 - - - +
6C VAL* 3.6 25.4 - - + +
7C GLU* 4.0 4.4 - - - +
424C ASN* 2.6 40.4 + - - +
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Residues in contact with HIS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.2 4.2 - - + +
45A TYR* 4.1 3.6 - - - -
46A ILE* 3.9 23.1 - - + +
421A VAL 4.8 0.4 - - - -
422A TYR* 3.4 31.4 - + + -
423A THR* 2.8 35.6 + - + +
425A ASP* 1.4 75.5 - - - +
427A MET* 1.3 66.9 + - + +
429A TYR* 3.2 5.9 + - - +
430A ILE* 3.1 29.6 + - + +
6C VAL* 3.3 18.1 - - + +
7C GLU* 3.1 34.5 + - + -
9C PHE 3.3 20.6 + - - -
10C ARG* 4.6 2.5 - - - -
11C ILE* 6.2 0.2 - - + -
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Residues in contact with MET 427 (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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48A LEU* 5.4 0.2 - - + -
331A GLN* 3.5 42.4 - - + +
334A TYR* 4.0 13.0 - - + -
335A LEU* 3.7 24.5 - - + +
417A ILE* 4.0 28.7 - - + -
422A TYR* 3.6 31.9 - - + -
423A THR 3.1 11.5 + - - +
424A ASN* 3.3 12.8 - - - +
426A HIS* 1.3 75.8 - - - +
428A ASP* 1.4 63.3 + - - +
430A ILE* 3.1 20.2 + - + +
431A ALA* 2.9 23.4 + - - +
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Residues in contact with ASP 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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4A ARG* 2.4 29.4 + - - -
334A TYR* 2.3 31.8 + - - -
338A ARG* 2.9 24.0 + - - +
424A ASN 2.8 11.9 + - - -
425A ASP* 3.8 11.4 - - - +
426A HIS 3.3 0.2 - - - -
427A MET* 1.4 71.7 - - - +
429A TYR* 1.3 54.2 + - - +
431A ALA* 4.4 1.1 - - - -
432A ASP* 2.7 46.3 + - - +
4C ARG* 5.3 1.4 - - - +
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Residues in contact with TYR 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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19A VAL* 4.1 11.3 - - + +
45A TYR* 3.5 28.5 - + - -
46A ILE* 3.7 16.6 - - + -
383A GLU 4.8 0.9 + - - -
384A SER* 2.6 48.9 + - - -
386A VAL* 3.9 6.5 - - + -
425A ASP 3.1 14.8 + - - +
426A HIS* 3.2 12.8 + - - +
428A ASP* 1.3 75.1 - - - +
430A ILE* 1.3 63.1 + - - +
432A ASP* 3.7 5.3 + - - +
433A ALA* 3.1 21.2 + - + +
6C VAL* 4.5 18.6 - - + -
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Residues in contact with ILE 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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46A ILE* 4.0 15.9 - - + -
48A LEU* 3.9 31.9 - - + -
335A LEU* 4.1 15.0 - - + -
339A LEU* 6.1 0.2 - - + -
380A LEU* 4.6 5.5 - - + +
386A VAL* 4.1 24.2 - - + -
415A LEU* 4.4 15.5 - - + -
426A HIS 3.1 22.8 + - - +
427A MET* 3.1 27.8 + - + +
429A TYR* 1.3 75.5 - - - +
431A ALA* 1.3 68.0 + - - +
433A ALA* 3.3 6.7 + - - +
434A LEU* 3.2 22.1 + - + +
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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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335A LEU* 4.1 7.6 - - + +
338A ARG* 3.8 42.8 - - + +
339A LEU* 3.9 19.5 - - + +
427A MET 2.9 18.5 + - - +
428A ASP* 4.4 0.4 - - - -
430A ILE* 1.3 71.8 - - - +
432A ASP* 1.3 58.6 + - - +
434A LEU* 3.3 1.6 + - - +
435A ILE* 2.9 36.2 + - + +
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Residues in contact with ASP 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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338A ARG* 3.2 28.9 + - - -
428A ASP* 2.7 30.4 + - - +
429A TYR* 4.1 5.1 + - - +
431A ALA* 1.3 70.2 - - - +
433A ALA* 1.3 54.4 + - - +
435A ILE* 3.7 7.2 - - - +
436A GLY* 2.9 31.9 + - - -
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Residues in contact with ALA 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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380A LEU* 3.7 11.4 - - + -
383A GLU* 5.3 6.6 - - + +
384A SER* 3.5 30.5 - - - -
429A TYR* 3.1 21.0 + - + +
430A ILE* 3.6 6.5 - - - +
432A ASP* 1.3 76.8 - - - +
434A LEU* 1.3 60.5 + - - +
436A GLY* 3.5 6.4 + - - -
437A LEU* 3.4 19.2 + - - +
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Residues in contact with LEU 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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339A LEU* 4.0 31.2 - - + -
344A ILE* 4.4 11.5 - - + +
357A VAL* 4.2 9.9 - - + -
362A LEU* 5.1 1.8 - - + -
376A VAL* 3.9 28.5 - - + -
380A LEU* 3.9 14.3 - - + +
413A MET* 3.6 26.0 - - + -
415A LEU* 4.7 4.7 - - + -
430A ILE* 3.2 13.2 + - + +
431A ALA 3.8 3.1 - - - +
433A ALA* 1.3 75.9 - - - +
435A ILE* 1.3 65.5 + - - +
437A LEU* 3.2 25.2 - - + +
438A LYS 3.9 0.7 + - - -
441A PHE* 3.8 17.8 - - + -
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Residues in contact with ILE 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 3.5 34.8 - - - +
339A LEU* 4.5 8.7 - - + -
342A ALA* 3.7 31.2 - - + -
344A ILE* 4.9 5.4 - - + -
431A ALA* 2.9 28.8 + - + +
432A ASP* 3.8 7.2 - - - +
434A LEU* 1.3 76.0 - - - +
436A GLY* 1.3 58.1 + - - +
438A LYS* 3.1 43.2 + - + +
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Residues in contact with GLY 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 ASP 2.9 16.8 + - - -
433A ALA 3.5 4.9 + - - -
434A LEU 3.3 0.6 - - - -
435A ILE* 1.3 75.5 - - - +
437A LEU* 1.3 60.3 + - - +
438A LYS* 3.3 0.8 + - - -
439A GLU* 4.8 8.1 + - - +
440A LYS* 4.8 11.6 + - - +
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Residues in contact with LEU 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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376A VAL* 4.5 3.8 - - + -
379A ALA* 4.2 12.6 - - + +
380A LEU* 4.0 23.3 - - - +
383A GLU* 3.8 38.1 - - + +
433A ALA 3.4 14.3 + - - +
434A LEU* 3.2 24.2 + - + +
435A ILE 3.1 0.2 - - - -
436A GLY* 1.3 77.9 - - - +
438A LYS* 1.3 65.2 + - - +
439A GLU 3.3 1.8 - - - -
440A LYS* 3.0 19.7 + - + +
441A PHE* 2.8 50.6 + - + -
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Residues in contact with LYS 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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342A ALA* 2.7 36.1 + - - +
343A GLY 6.0 0.4 - - - -
344A ILE* 4.6 13.0 - - + -
435A ILE* 3.1 34.9 + - + +
436A GLY 3.3 0.6 - - - -
437A LEU* 1.3 77.2 - - - +
439A GLU* 1.3 70.7 + - + +
441A PHE* 3.3 31.8 + - + +
442A ALA 4.5 0.2 + - - -
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Residues in contact with GLU 439 (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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436A GLY 4.8 6.0 + - - +
437A LEU 3.3 0.6 - - - -
438A LYS* 1.3 81.2 - - + +
440A LYS* 1.3 59.0 + - - +
441A PHE 3.0 4.7 + - - -
442A ALA* 3.6 16.3 + - - +
443A THR* 5.1 1.7 - - - +
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Residues in contact with LYS 440 (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 ALA* 6.4 1.3 - - + -
383A GLU* 4.4 30.2 + - - +
436A GLY 4.8 9.5 + - - +
437A LEU* 3.3 23.9 - - + +
439A GLU* 1.3 78.1 - - - +
441A PHE* 1.3 61.3 + - - +
442A ALA 3.3 0.8 + - - -
443A THR* 3.0 34.0 + - + +
444A LEU* 3.9 10.8 + - + +
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Residues in contact with PHE 441 (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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344A ILE* 4.5 6.3 - - + -
362A LEU* 3.4 43.5 - - + +
363A VAL* 3.2 21.1 - - + +
365A GLN* 3.1 8.5 + - - -
376A VAL* 3.7 18.6 - - + -
434A LEU* 3.8 22.9 - - + -
437A LEU* 2.8 48.8 + - + -
438A LYS* 3.3 38.8 - - + +
439A GLU 3.0 0.8 + - - -
440A LYS* 1.3 74.1 - - - +
442A ALA* 1.3 58.9 + - - +
444A LEU* 2.9 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
------------------------------------------------------------
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