Contacts of the helix formed by residues 424 - 441 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B ASP* 3.1 28.5 + - - +
4D ARG* 3.4 32.2 + - + +
5D ILE 3.3 31.9 + - - +
7D GLU* 4.6 2.8 + - - -
327D TYR* 4.6 6.5 - - - -
331D GLN* 3.2 31.7 + - - +
334D TYR* 3.9 10.2 - - + +
423D THR* 1.3 71.4 - - - +
425D ASP* 1.4 55.2 + - - +
427D MET* 3.0 11.3 + - - +
428D ASP* 2.8 25.8 + - - -
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Residues in contact with ASP 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 2.8 32.3 + - - +
5B ILE 4.0 3.1 - - - +
6B VAL* 3.6 23.3 - - + +
7B GLU* 3.9 10.8 - - - +
424B ASN* 2.8 39.8 + - - +
4D ARG* 2.9 12.2 + - - +
423D THR* 3.1 10.3 + - - +
424D ASN* 1.4 75.5 - - - +
426D HIS* 1.4 63.9 + - - +
428D ASP* 3.3 8.7 + - - +
429D TYR* 3.1 16.8 + - - +
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Residues in contact with HIS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.4 18.4 - - + -
7B GLU* 3.2 29.7 + - + +
9B PHE 3.2 20.1 + - - -
10B ARG* 4.5 4.0 - - - -
11B ILE* 6.1 0.2 - - + -
17D ILE* 4.1 4.7 - - + +
45D TYR* 4.0 3.8 - - - -
46D ILE* 3.9 25.5 - - + +
421D VAL 4.7 0.4 - - - -
422D TYR* 3.5 29.6 - + + -
423D THR* 2.8 44.6 + - + +
425D ASP* 1.4 72.9 - - - +
427D MET* 1.3 68.0 + - + +
429D TYR* 3.1 6.7 + - - +
430D ILE* 3.0 27.3 + - + +
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Residues in contact with MET 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D GLN* 3.6 41.3 - - + +
334D TYR* 4.1 13.5 - - + -
335D LEU* 3.8 34.9 - - + +
338D ARG* 5.9 0.2 - - - -
417D ILE* 4.2 18.8 - - + -
422D TYR* 3.6 31.9 - - + -
423D THR 3.1 9.4 + - - +
424D ASN* 3.0 21.0 + - - +
426D HIS* 1.3 76.7 - - - +
428D ASP* 1.3 60.4 + - - +
430D ILE* 3.0 28.1 + - + +
431D ALA* 3.1 14.7 + - - +
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Residues in contact with ASP 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 4.8 2.9 + - - +
4D ARG* 2.6 27.2 + - - -
334D TYR* 2.3 31.1 + - - -
338D ARG* 2.8 23.8 + - - +
424D ASN 2.8 11.3 + - - -
425D ASP* 3.3 13.0 + - - +
427D MET* 1.3 71.4 - - - +
429D TYR* 1.3 56.3 + - - +
431D ALA* 4.5 0.9 - - - -
432D ASP* 2.9 40.8 + - - +
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Residues in contact with TYR 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.4 18.8 - - + -
19D VAL* 3.7 17.7 - - + +
25D ARG* 5.4 0.2 + - - -
45D TYR* 3.5 31.2 - + - -
46D ILE* 3.9 8.5 - - + -
383D GLU 4.9 0.5 + - - -
384D SER* 2.7 47.5 + - - -
386D VAL* 3.9 7.4 - - + -
425D ASP 3.1 13.0 + - - +
426D HIS* 3.3 12.8 - - - +
428D ASP* 1.3 76.3 - - - +
430D ILE* 1.3 65.0 + - - +
432D ASP* 4.5 3.9 - - - +
433D ALA* 3.1 22.3 + - + +
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Residues in contact with ILE 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 4.0 11.9 - - + -
48D LEU* 3.6 45.5 - - + -
335D LEU* 4.2 14.6 - - + -
380D LEU* 4.5 6.2 - - + +
386D VAL* 4.2 24.2 - - + -
415D LEU* 4.2 16.8 - - + -
426D HIS 3.0 17.0 + - - +
427D MET* 3.0 28.0 + - + +
429D TYR* 1.3 78.7 - - - +
431D ALA* 1.3 62.4 + - - +
433D ALA* 3.4 3.3 + - - +
434D LEU* 3.0 22.6 + - + +
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LEU* 4.0 7.8 - - + +
338D ARG* 3.9 37.7 - - + +
339D LEU* 3.8 21.3 - - + -
427D MET 3.1 14.2 + - - +
428D ASP 4.0 2.5 - - - +
430D ILE* 1.3 74.1 - - - +
432D ASP* 1.3 61.3 + - - +
434D LEU* 2.8 5.0 + - - +
435D ILE* 2.7 34.2 + - + +
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Residues in contact with ASP 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ARG* 2.7 35.1 + - - -
428D ASP* 2.9 31.8 + - - +
429D TYR* 4.5 3.2 - - - +
431D ALA* 1.3 71.4 - - - +
433D ALA* 1.3 62.9 + - - +
435D ILE* 3.7 8.1 - - - +
436D GLY* 2.9 22.5 + - - -
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Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D LEU* 3.9 13.2 - - + -
383D GLU* 5.3 6.3 - - + +
384D SER* 3.5 31.6 - - - -
429D TYR* 3.1 22.7 + - + +
430D ILE* 3.9 2.0 - - - +
432D ASP* 1.3 77.0 - - - +
434D LEU* 1.3 62.8 + - - +
436D GLY* 3.3 8.5 + - - -
437D LEU* 3.6 17.7 + - - +
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Residues in contact with LEU 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D LEU* 3.8 30.3 - - + -
344D ILE* 4.2 23.5 - - + +
357D VAL* 4.3 4.0 - - + -
362D LEU* 4.9 1.8 - - + -
376D VAL* 4.3 10.3 - - + -
380D LEU* 4.1 12.1 - - + +
413D MET* 3.7 33.4 - - + -
415D LEU* 4.7 4.5 - - + -
430D ILE* 3.0 13.2 + - + +
431D ALA 2.8 13.3 + - - +
433D ALA* 1.3 74.3 - - - +
435D ILE* 1.3 58.5 + - - +
437D LEU* 3.3 21.4 + - + +
441D PHE* 3.6 26.9 - - + -
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Residues in contact with ILE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ARG* 3.7 36.1 - - - +
339D LEU* 4.6 2.5 - - + -
342D ALA* 3.4 35.2 - - + -
344D ILE* 4.5 17.5 - - + -
431D ALA* 2.7 26.7 + - + +
432D ASP* 3.9 6.3 - - - +
434D LEU* 1.3 73.8 - - - +
436D GLY* 1.3 58.4 + - - +
437D LEU 3.2 1.4 + - - -
438D LYS* 3.5 27.9 + - + +
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Residues in contact with GLY 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D GLU* 5.8 2.0 - - - +
432D ASP 2.9 15.2 + - - -
433D ALA* 3.3 4.9 + - - -
434D LEU 3.2 0.6 - - - -
435D ILE* 1.3 75.9 - - - +
437D LEU* 1.3 63.9 + - - +
438D LYS* 3.4 0.7 - - - -
439D GLU* 4.7 8.1 + - - +
440D LYS* 5.1 7.1 - - - +
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Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D VAL 4.4 2.5 - - - +
379D ALA* 3.8 13.0 - - + +
380D LEU* 3.7 33.0 - - + +
383D GLU* 3.5 44.4 - - + +
433D ALA 3.7 13.2 - - - +
434D LEU* 3.3 8.5 + - + +
435D ILE 3.2 0.8 - - - -
436D GLY* 1.3 78.7 - - - +
438D LYS* 1.3 53.5 + - - +
439D GLU 3.2 3.1 - - - -
440D LYS* 2.6 41.7 + - + -
441D PHE* 3.0 44.1 + - + -
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Residues in contact with LYS 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ALA* 2.4 32.6 + - - +
343D GLY* 4.4 6.9 + - - -
344D ILE* 3.9 20.9 - - + -
435D ILE* 3.5 26.6 + - + +
436D GLY 3.4 0.8 - - - -
437D LEU* 1.3 77.0 - - - +
439D GLU* 1.3 67.6 + - + +
441D PHE* 3.3 34.8 + - + +
442D ALA* 4.4 2.6 + - - +
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Residues in contact with GLU 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D GLY 5.2 6.5 - - - +
437D LEU 2.9 2.6 + - - -
438D LYS* 1.3 78.4 - - + +
440D LYS* 1.3 63.8 + - + +
441D PHE 3.6 0.3 + - - -
442D ALA* 4.1 13.2 + - - +
443D THR* 4.6 6.1 + - - +
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Residues in contact with LYS 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ARG* 4.3 5.1 - - - +
379D ALA* 6.5 0.9 - - + -
383D GLU* 3.0 42.7 + - - +
436D GLY 5.1 5.6 - - - +
437D LEU* 2.6 27.3 + - + +
439D GLU* 1.3 73.5 - - + +
441D PHE* 1.3 66.7 + - + +
442D ALA 3.2 2.5 - - - -
443D THR* 3.0 26.1 + - - +
444D LEU* 3.4 11.1 + - + +
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Residues in contact with PHE 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D ILE* 4.6 4.5 - - + -
362D LEU* 3.0 50.9 - - + +
363D VAL* 3.5 5.8 - - + +
365D GLN* 2.8 26.3 + - - -
376D VAL* 4.2 15.7 - - + -
434D LEU* 3.6 23.8 - - + -
437D LEU* 3.0 42.4 + - + -
438D LYS* 3.3 46.4 + - + +
440D LYS* 1.3 75.8 - - - +
442D ALA* 1.3 50.5 + - - +
444D LEU* 2.9 30.9 + - + +
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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
------------------------------------------------------------
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