Contacts of the helix formed by residues 424 - 443 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ASP* 2.6 29.9 + - - +
4C ARG* 3.5 32.6 + - + +
5C ILE 3.2 31.3 + - - +
7C GLU* 4.5 3.5 + - - -
327C TYR* 4.6 4.4 - - - -
331C GLN* 3.2 33.0 + - - +
334C TYR* 3.8 9.8 - - + +
423C THR* 1.3 74.5 - - - +
425C ASP* 1.4 55.6 + - - +
426C HIS 3.3 0.2 - - - -
427C MET* 3.2 10.2 + - - +
428C ASP* 2.9 23.2 + - - -
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Residues in contact with ASP 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 3.0 19.5 + - - +
5A ILE 3.8 2.9 - - - +
6A VAL* 3.6 26.8 - - + +
7A GLU* 4.0 6.0 - - - +
424A ASN* 2.7 39.0 + - - +
4C ARG* 2.7 27.6 + - - +
423C THR* 3.1 9.4 + - - +
424C ASN* 1.4 74.4 - - - +
426C HIS* 1.4 62.6 + - - +
428C ASP* 3.4 8.5 + - - +
429C TYR* 3.0 25.1 + - - +
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Residues in contact with HIS 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.3 17.7 - - + +
7A GLU* 3.1 28.4 + - + -
9A PHE 3.3 21.7 + - - -
10A ARG* 4.5 3.4 - - - -
11A ILE* 6.2 0.2 - - + -
17C ILE* 3.9 5.9 - - + +
45C TYR* 4.0 4.7 - - - -
46C ILE* 3.9 25.8 - - + +
422C TYR* 3.5 29.6 - + + -
423C THR* 3.0 41.3 + - + +
425C ASP* 1.4 79.1 - - - +
427C MET* 1.3 57.1 + - + +
429C TYR* 3.1 6.3 + - - +
430C ILE* 3.0 33.6 + - + +
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Residues in contact with MET 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C GLN* 3.7 45.8 - - + +
334C TYR* 4.1 13.2 - - + -
335C LEU* 3.9 24.6 - - + +
338C ARG* 6.2 0.2 - - - -
417C ILE* 4.1 30.3 - - + -
422C TYR* 3.7 32.5 - - + -
423C THR 3.2 7.7 + - - +
424C ASN* 3.2 14.6 + - - +
426C HIS* 1.3 74.0 - - - +
428C ASP* 1.4 62.9 + - - +
430C ILE* 2.9 28.9 + - + +
431C ALA* 2.9 14.6 + - - +
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Residues in contact with ASP 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 5.3 1.0 - - - -
4C ARG* 2.5 28.2 + - - -
334C TYR* 2.4 30.0 + - - -
338C ARG* 3.0 23.0 + - - +
424C ASN 2.9 8.6 + - - +
425C ASP* 3.7 12.6 - - - +
426C HIS 3.3 0.2 - - - -
427C MET* 1.4 73.6 - - - +
429C TYR* 1.3 58.5 + - - +
431C ALA* 4.5 0.9 - - - +
432C ASP* 2.8 41.8 + - - +
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Residues in contact with TYR 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.9 14.1 - - + -
19C VAL* 4.2 12.8 - - + +
45C TYR* 3.6 31.3 - + - -
46C ILE* 3.8 15.5 - - + -
384C SER* 2.7 44.0 + - - -
386C VAL* 3.7 13.5 - - + -
425C ASP 3.0 13.8 + - - +
426C HIS* 3.1 12.3 + - - +
428C ASP* 1.3 77.2 - - - +
430C ILE* 1.3 65.8 + - - +
432C ASP* 4.0 4.9 - - - +
433C ALA* 3.1 21.3 + - + +
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Residues in contact with ILE 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.0 20.4 - - + -
48C LEU* 3.6 35.4 - - + -
335C LEU* 4.0 15.0 - - + -
339C LEU* 6.1 0.2 - - + -
380C LEU* 4.8 5.9 - - + +
386C VAL* 4.2 16.8 - - + -
415C LEU* 4.2 16.2 - - + -
426C HIS 3.0 15.6 + - - +
427C MET* 2.9 35.6 + - + +
429C TYR* 1.3 79.5 - - - +
431C ALA* 1.3 63.6 + - - +
433C ALA* 3.1 15.6 + - - +
434C LEU* 3.2 14.0 + - + +
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 4.0 11.2 - - + +
338C ARG* 3.8 42.0 - - + +
339C LEU* 4.0 17.0 - - + -
427C MET 2.9 14.7 + - - +
428C ASP* 4.5 0.4 - - - -
430C ILE* 1.3 76.0 - - - +
432C ASP* 1.3 62.9 + - - +
434C LEU* 3.1 3.8 + - - +
435C ILE* 2.9 29.6 + - + +
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Residues in contact with ASP 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C ARG* 2.8 37.6 + - - -
428C ASP* 2.8 29.5 + - - +
429C TYR* 4.2 5.0 - - - +
431C ALA* 1.3 71.9 - - - +
433C ALA* 1.3 61.1 + - - +
435C ILE* 4.0 5.8 - - - +
436C GLY* 3.0 21.7 + - - -
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Residues in contact with ALA 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU* 3.7 11.2 - - + -
383C GLU* 4.8 7.3 - - + +
384C SER* 3.5 31.6 - - - -
386C VAL* 5.4 0.2 - - + -
429C TYR* 3.1 19.4 + - + +
430C ILE* 3.1 7.1 + - - +
432C ASP* 1.3 77.8 - - - +
434C LEU* 1.3 61.0 + - - +
436C GLY* 3.7 2.2 + - - -
437C LEU* 3.5 23.9 + - - +
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Residues in contact with LEU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C LEU* 3.9 33.0 - - + -
344C ILE* 4.5 13.9 - - + +
357C VAL* 4.2 6.3 - - + -
362C LEU* 4.8 2.5 - - + -
376C VAL* 4.3 8.7 - - + -
380C LEU* 4.2 14.5 - - + +
413C MET* 3.6 34.3 - - + -
415C LEU* 4.5 6.3 - - + -
430C ILE* 3.2 9.2 + - + +
431C ALA 3.1 7.0 + - - +
433C ALA* 1.3 74.8 - - - +
435C ILE* 1.3 68.3 + - - +
436C GLY 3.2 0.2 - - - -
437C LEU* 3.0 26.4 + - + +
438C LYS 3.8 1.9 + - - -
441C PHE* 3.9 24.7 - - + -
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Residues in contact with ILE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C ARG* 3.6 37.5 - - - +
339C LEU* 4.3 10.5 - - + -
342C ALA* 3.6 34.3 - - + -
344C ILE* 4.5 6.1 - - + -
431C ALA* 2.9 24.4 + - + +
432C ASP* 4.0 5.4 - - - +
434C LEU* 1.3 73.4 - - - +
436C GLY* 1.3 58.3 + - - +
438C LYS* 2.9 45.7 + - + +
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Residues in contact with GLY 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C GLU* 6.1 0.2 - - - -
432C ASP 3.0 17.9 + - - -
433C ALA* 3.9 3.8 - - - -
434C LEU 3.2 0.2 - - - -
435C ILE* 1.3 77.5 - - - +
437C LEU* 1.3 59.0 + - - +
438C LYS 3.2 1.6 + - - -
439C GLU* 4.6 3.6 + - - +
440C LYS* 3.8 15.0 + - - +
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C VAL 4.8 1.6 - - - +
379C ALA* 3.9 15.9 - - + +
380C LEU* 3.7 36.1 - - + +
383C GLU* 3.3 20.6 - - + +
433C ALA 3.5 13.0 + - - +
434C LEU* 3.0 16.5 + - + +
435C ILE 2.9 0.4 + - - -
436C GLY* 1.3 75.6 - - - +
438C LYS* 1.3 58.3 + - - +
439C GLU 3.3 2.7 - - - -
440C LYS* 2.9 56.2 + - + +
441C PHE* 3.0 34.4 + - + -
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Residues in contact with LYS 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C ALA* 2.5 34.2 + - - +
343C GLY* 4.7 5.7 - - - -
344C ILE* 4.3 12.8 - - + -
362C LEU* 6.1 0.2 - - + -
435C ILE* 2.9 30.4 + - + +
436C GLY 3.2 1.0 - - - -
437C LEU* 1.3 77.7 - - - +
439C GLU* 1.3 64.9 + - + +
440C LYS 3.3 2.1 + - - -
441C PHE* 3.5 33.2 + - + +
442C ALA* 4.7 1.6 + - - +
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Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLY 4.6 3.0 + - - +
437C LEU 3.3 0.6 - - - -
438C LYS* 1.3 80.6 - - + +
440C LYS* 1.3 63.7 + - + +
441C PHE 3.5 0.4 - - - -
442C ALA* 4.9 6.9 - - - +
443C THR* 4.6 8.3 - - - +
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Residues in contact with LYS 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C GLU* 3.3 26.1 + - - +
436C GLY 3.8 14.5 + - - +
437C LEU* 2.9 43.6 + - + +
439C GLU* 1.3 80.3 - - + +
441C PHE* 1.3 70.8 + - + +
442C ALA 3.2 2.5 - - - -
443C THR* 3.1 27.0 + - - +
444C LEU* 3.6 14.2 + - + +
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Residues in contact with PHE 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ILE* 4.2 10.5 - - + -
362C LEU* 3.3 66.6 - - + +
363C VAL* 3.6 4.9 - - + +
365C GLN* 2.9 17.5 + - - -
376C VAL* 4.1 17.7 - - + -
434C LEU* 3.9 24.0 - - + -
437C LEU* 3.0 28.3 + - + -
438C LYS* 3.5 31.0 - - + +
439C GLU 3.5 0.8 - - - -
440C LYS* 1.3 76.4 - - - +
442C ALA* 1.3 63.5 + - - +
444C LEU* 2.9 31.0 + - + +
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Residues in contact with ALA 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C LEU 4.9 0.8 + - - -
364C PRO* 6.4 0.2 - - - -
365C GLN* 3.1 24.2 + - - +
438C LYS 4.7 1.8 + - - +
439C GLU 4.9 6.5 - - - +
440C LYS 4.9 0.7 - - - -
441C PHE* 1.3 77.4 - - - +
443C THR* 1.3 64.0 + - + +
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Residues in contact with THR 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C GLU 4.6 7.0 - - - +
440C LYS* 3.1 18.6 + - - +
442C ALA* 1.3 79.5 - - + +
444C LEU* 1.3 68.8 + - - +
445C LYS* 2.8 32.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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