Contacts of the helix formed by residues 457 - 460 (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 ARG 457 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PHE* 3.5 11.5 - - - -
393B SER 3.1 26.3 + - - -
394B PHE* 3.0 21.0 + - - +
395B LEU 6.1 0.2 - - - +
397B GLY* 3.3 22.2 - - - -
398B ARG* 4.6 7.9 - - - +
405B GLN* 3.1 19.8 + - - -
449B PHE* 2.9 53.1 - - - -
452B GLU* 3.3 20.2 + - - +
453B PRO* 3.4 41.5 - - + +
455B VAL 3.2 0.4 + - - -
456B LEU* 1.3 74.8 - - - +
458B HIS* 1.3 63.4 + - - +
459B PHE 3.2 1.1 - - - -
461B ALA* 2.8 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN* 3.3 18.2 + - - +
37B PHE* 3.9 23.7 - + - -
133B ASP* 4.7 6.3 - - - -
389B VAL* 4.5 8.4 - - + +
390B GLU* 4.6 10.4 + - + -
391B ILE* 5.9 0.8 - - - +
394B PHE* 3.8 25.8 - + + +
395B LEU* 3.4 56.2 - - + +
456B LEU* 3.2 4.1 - - - +
457B ARG* 1.3 81.0 - - + +
459B PHE* 1.3 97.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 5.7 1.6 - + - -
293A VAL* 3.3 39.7 - - + -
298A PHE* 3.7 33.6 - + + -
35B ASN* 3.7 2.0 + - - -
37B PHE* 3.7 39.3 - + - +
38B LEU* 3.7 13.7 - - - +
101B ARG* 5.7 2.7 - - - -
133B ASP* 6.1 0.7 - - + -
456B LEU* 3.6 31.3 + - + +
457B ARG 3.2 0.4 - - - -
458B HIS* 1.3 109.5 + + - +
460B THR* 1.3 66.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 4.3 22.4 - - - +
298A PHE* 5.8 0.9 - - + -
299A VAL* 5.4 7.0 - - + -
35B ASN* 3.9 2.0 - - - +
38B LEU* 3.9 26.2 - - + +
451B TYR* 3.6 16.4 + - - -
453B PRO* 3.7 17.9 - - - +
455B VAL 5.2 0.2 + - - -
456B LEU 3.8 6.8 + - - -
457B ARG 3.4 2.4 + - - -
459B PHE* 1.3 84.7 - - + +
461B ALA* 1.3 68.5 + - - +
462B ARG* 3.5 3.5 + - - +
----------------------------------------------------------
Back to top of page
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