Contacts of the helix formed by residues 418 - 424 (chain B) in PDB entry 2AX1
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 THR 418 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383B TYR* 3.8 9.9 - - + -
384B LEU 3.4 22.2 - - - +
385B THR* 3.3 25.4 - - - +
415B TYR* 2.7 30.5 + - + +
417B PRO* 1.3 77.4 - - - +
419B LEU* 1.3 64.8 + - - +
420B TRP* 3.5 21.8 - - - +
421B ALA* 3.1 19.4 + - - +
422B ARG* 3.1 24.1 + - - +
477B TYR* 4.4 0.2 - - - -
481B GLU* 4.9 0.2 - - - -
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Residues in contact with LEU 419 (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 TYR* 5.2 0.6 + - - -
418B THR* 1.3 74.6 - - - +
420B TRP* 1.3 62.3 + - + +
422B ARG* 4.7 2.9 - - - +
423B MET* 3.0 46.8 + - - +
477B TYR* 3.7 57.6 - - + -
481B GLU* 4.4 9.8 + - + -
482B ILE* 4.0 24.7 - - + -
485B VAL* 3.9 23.8 - - + -
497B LEU* 3.6 32.5 - - + -
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Residues in contact with TRP 420 (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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385B THR* 3.0 18.6 + - - -
386B ARG* 3.3 36.9 + - + -
388B PRO* 3.6 24.5 - - + -
391B PRO* 3.9 22.2 - - + -
392B LEU* 5.6 3.5 - - + +
411B ASN* 4.7 2.5 - - + -
415B TYR* 3.6 38.6 - + + -
418B THR* 3.5 11.2 - - + -
419B LEU* 1.3 82.5 - - - +
421B ALA* 1.3 78.6 + - + +
424B ILE* 3.0 44.6 + - + +
425B LEU* 3.2 28.1 + - + +
481B GLU* 3.7 13.2 - - - -
485B VAL* 3.9 26.5 - - + -
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Residues in contact with ALA 421 (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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412B ILE* 4.5 9.4 - - - +
415B TYR* 3.2 20.6 - - + +
416B ALA* 4.4 5.2 - - - -
418B THR* 3.1 22.2 + - - +
420B TRP* 1.3 92.5 - - + +
422B ARG* 1.3 55.9 + - - +
425B LEU* 3.4 14.8 + - + +
426B MET* 2.8 38.3 + - + +
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Residues in contact with ARG 422 (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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416B ALA 3.0 27.8 - - - +
417B PRO 3.7 2.9 - - - -
418B THR 3.1 15.6 + - - +
419B LEU* 4.1 2.9 - - - +
421B ALA* 1.3 76.8 - - - +
423B MET* 1.3 66.3 + - + +
426B MET* 3.3 35.8 - - + +
427B THR* 3.7 1.7 + - - -
471B ALA 3.2 16.7 + - - +
472B PHE* 3.1 31.3 + - - +
473B SER* 3.8 1.8 - - - +
474B LEU* 2.8 34.1 + - - +
477B TYR* 3.0 19.2 + - - -
524B TYR 5.6 0.4 + - - -
525B LEU 5.2 1.2 + - - -
526B PHE* 4.6 0.3 - - - -
528B TRP* 3.5 54.4 + - + +
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Residues in contact with MET 423 (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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419B LEU* 3.0 33.1 + - - +
422B ARG* 1.3 78.9 - - + +
424B ILE* 1.3 59.6 + - - +
427B THR* 2.8 20.8 + - - -
477B TYR* 6.1 0.9 - - - -
497B LEU* 3.7 45.3 - - + +
500B TRP* 3.4 15.6 - - + +
501B ARG* 3.6 27.4 - - - +
528B TRP* 3.5 39.2 - - + -
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Residues in contact with ILE 424 (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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30B LEU* 3.7 28.3 - - + -
392B LEU* 3.7 19.7 - - + -
420B TRP* 3.0 26.1 + - + +
423B MET* 1.3 80.3 - - - +
425B LEU* 1.3 61.1 + - + +
426B MET 3.4 0.4 - - - -
427B THR* 3.4 1.4 + - - -
428B HIS* 2.8 32.9 + - - +
485B VAL* 4.8 0.2 - - + -
489B LEU* 3.6 42.0 - - + -
494B VAL* 4.3 3.6 - - + -
497B LEU* 4.2 11.4 - - + -
500B TRP* 3.9 26.5 - - + +
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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
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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