Contacts of the helix formed by residues 424 - 437 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.5 23.4 - - + +
5B ILE 3.4 30.1 + - - +
7B GLU* 4.6 2.2 + - - -
327B TYR* 4.6 5.9 - - - -
331B GLN* 3.1 36.3 + - - +
334B TYR* 4.0 11.7 - - + -
423B THR* 1.3 75.6 - - - +
425B ASP* 1.4 54.5 + - - +
427B MET* 3.1 10.2 + - - +
428B ASP* 2.8 30.1 + - - +
425D ASP* 2.8 29.1 + - - +
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Residues in contact with ASP 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 2.8 14.3 + - - +
423B THR* 3.1 10.4 + - - +
424B ASN* 1.4 71.9 - - - +
426B HIS* 1.3 65.1 + - - +
428B ASP* 3.3 8.6 + - - +
429B TYR* 3.1 20.8 + - - +
4D ARG* 2.8 33.3 + - - +
5D ILE 4.2 1.3 - - - +
6D VAL* 3.7 29.9 - - + +
7D GLU* 4.0 5.5 - - - +
423D THR* 5.8 0.2 - - - -
424D ASN* 3.1 39.5 + - - +
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Residues in contact with HIS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.8 5.5 - - + +
45B TYR* 4.0 3.8 - - - -
46B ILE* 3.8 27.3 - - + +
421B VAL 4.9 0.2 - - - -
422B TYR* 3.5 29.4 - + + -
423B THR* 2.9 44.4 + - + +
425B ASP* 1.3 75.7 - - - +
427B MET* 1.3 65.8 - - + +
429B TYR* 3.1 13.3 + - - +
430B ILE* 3.1 18.0 + - + +
6D VAL* 3.3 16.3 - - + +
7D GLU* 3.1 31.0 + - + -
9D PHE 3.4 20.2 + - - -
10D ARG* 4.7 3.1 - - - -
11D ILE* 6.4 0.4 - - + -
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Residues in contact with MET 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 5.2 0.2 - - + -
331B GLN* 3.7 39.3 - - + +
334B TYR* 4.1 13.2 - - + -
335B LEU* 3.9 24.3 - - + +
417B ILE* 4.1 29.4 - - + -
422B TYR* 3.6 32.5 - - + -
423B THR 3.1 12.4 + - - +
424B ASN* 3.1 14.5 + - - +
426B HIS* 1.3 75.6 - - - +
428B ASP* 1.4 64.0 + - - +
430B ILE* 3.0 22.7 + - + +
431B ALA* 2.9 24.5 + - - +
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Residues in contact with ASP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 2.5 27.8 + - - -
334B TYR* 2.3 31.0 + - - -
338B ARG* 3.1 22.0 + - - +
424B ASN 2.8 10.7 + - - -
425B ASP* 3.6 14.2 - - - +
426B HIS 3.2 0.2 - - - -
427B MET* 1.4 72.3 - - - +
429B TYR* 1.4 59.8 + - - +
431B ALA* 4.5 0.7 - - - -
432B ASP* 2.8 41.6 + - - +
4D ARG* 4.8 2.6 + - - +
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Residues in contact with TYR 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.3 12.1 - - + +
45B TYR* 3.7 29.1 - + - -
46B ILE* 3.7 16.4 - - + -
384B SER* 2.7 43.4 + - - -
386B VAL* 3.8 14.4 - - + -
425B ASP 3.1 13.6 + - - +
426B HIS* 3.1 13.0 + - - +
428B ASP* 1.4 79.4 - - - +
430B ILE* 1.3 59.3 + - - +
432B ASP* 3.9 3.6 - - - +
433B ALA* 3.0 25.8 + - + +
6D VAL* 5.0 12.8 - - + -
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Residues in contact with ILE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 4.0 17.0 - - + -
48B LEU* 3.6 36.8 - - + -
335B LEU* 4.0 15.7 - - + -
380B LEU* 4.8 5.0 - - + +
386B VAL* 4.2 19.7 - - + -
415B LEU* 4.1 16.4 - - + -
426B HIS 3.1 15.5 + - - +
427B MET* 3.0 34.6 + - + +
429B TYR* 1.3 80.5 - - - +
431B ALA* 1.3 65.9 + - - +
433B ALA* 3.2 6.5 + - - +
434B LEU* 3.0 23.2 + - + +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU* 3.9 14.8 - - + -
338B ARG* 3.9 37.0 - - + +
339B LEU* 3.9 16.2 - - + -
427B MET 2.9 15.1 + - - +
428B ASP* 4.5 0.4 - - - -
430B ILE* 1.3 76.9 - - - +
432B ASP* 1.3 63.3 + - - +
434B LEU* 3.1 2.8 + - - +
435B ILE* 2.9 31.7 + - + +
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Residues in contact with ASP 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG* 2.7 40.5 + - - -
428B ASP* 2.8 30.3 + - - +
429B TYR* 4.2 3.9 - - - +
431B ALA* 1.3 70.7 - - - +
433B ALA* 1.3 60.9 + - - +
435B ILE* 3.8 5.1 - - - +
436B GLY* 2.9 22.0 + - - -
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LEU* 3.9 11.1 - - + +
383B GLU* 5.2 6.5 - - + +
384B SER* 3.6 31.4 - - - -
429B TYR* 3.0 20.3 + - + +
430B ILE* 3.2 6.7 + - - +
432B ASP* 1.3 75.2 - - - +
434B LEU* 1.3 65.3 + - - +
436B GLY* 3.5 2.9 + - - -
437B LEU* 3.4 21.3 + - - +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B LEU* 3.7 34.3 - - + -
344B ILE* 4.3 13.0 - - + -
357B VAL* 4.0 7.9 - - + -
362B LEU* 5.3 1.1 - - + -
376B VAL* 4.4 6.3 - - + -
380B LEU* 4.2 13.4 - - + +
413B MET* 3.8 33.4 - - + -
415B LEU* 4.4 6.7 - - + -
430B ILE* 3.0 17.4 + - + +
431B ALA 3.7 2.9 - - - +
433B ALA* 1.3 73.9 - - - +
435B ILE* 1.3 57.5 + - - +
437B LEU* 2.8 42.4 + - + +
438B LYS 3.7 2.1 + - - -
441B PHE* 4.0 23.6 - - + -
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG* 3.6 39.5 - - - +
339B LEU* 4.4 9.9 - - + -
342B ALA* 3.7 33.7 - - + -
344B ILE* 4.5 11.2 - - + -
431B ALA* 2.9 25.4 + - + +
432B ASP* 4.0 5.2 - - - +
434B LEU* 1.3 73.3 - - - +
436B GLY* 1.3 56.3 + - - +
438B LYS* 3.0 36.3 + - + +
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Residues in contact with GLY 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B GLU* 5.7 0.8 - - - +
432B ASP 2.9 17.3 + - - -
433B ALA* 3.8 5.2 - - - -
434B LEU 3.2 0.4 - - - -
435B ILE* 1.3 74.6 - - - +
437B LEU* 1.3 57.8 + - - +
438B LYS 3.4 0.4 - - - -
439B GLU* 5.1 1.7 + - - +
440B LYS* 4.4 12.8 + - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B VAL* 4.7 2.0 - - + +
379B ALA* 4.1 14.1 - - + -
380B LEU* 3.8 37.0 - - + +
383B GLU* 3.4 29.2 - - + -
433B ALA 3.4 13.0 + - - +
434B LEU* 2.8 23.1 + - + +
436B GLY* 1.3 71.5 - - - +
438B LYS* 1.3 65.1 + - - +
439B GLU 3.3 3.1 - - - -
440B LYS* 2.9 40.7 + - + +
441B PHE* 3.3 32.9 + - + -
444B LEU* 6.1 0.2 - - + -
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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