Contacts of the helix formed by residues 450 - 457 (chain B) in PDB entry 1ZDT
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 450 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B CYS* 3.7 21.8 + - - +
270B ASP* 3.6 17.6 + - - -
446B MET* 3.5 25.2 - - + +
447B PRO* 3.3 25.5 - - + +
448B ARG 3.2 4.7 + - - +
449B ASN* 1.3 76.9 - - - +
451B LEU* 1.3 60.9 + - - +
452B LEU* 3.2 27.9 + - - +
453B ILE* 3.2 27.6 + - + +
454B GLU* 3.4 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASP* 3.1 49.5 + - + +
271B GLN* 5.7 0.2 - - - +
273B PHE* 3.5 34.1 - - + -
274B ILE* 4.1 29.8 - - + -
449B ASN 3.3 5.4 + - - +
450B ASN* 1.3 69.6 - - - +
452B LEU* 1.3 61.4 + - - +
453B ILE 3.1 1.8 - - - -
454B GLU* 3.2 11.1 + - + +
455B MET* 2.9 32.5 + - + +
744Q LEU* 4.5 25.4 - - + -
748Q LEU* 4.4 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B CYS 5.6 0.4 - - - +
269B ALA* 4.2 23.3 - - + +
270B ASP* 3.4 17.0 + - - +
273B PHE* 4.1 20.9 - - + -
302B TRP* 3.6 17.6 - - + -
306B LEU* 3.7 31.4 - - + -
437B LEU* 4.3 22.9 - - + -
446B MET* 6.0 0.7 - - + -
450B ASN* 3.2 10.4 + - - +
451B LEU* 1.3 78.7 - - + +
453B ILE* 1.3 52.9 + - - +
455B MET* 3.3 7.3 + - + +
456B LEU* 2.7 33.2 + - - +
1002B PEF 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 4.0 22.2 - - + +
441B HIS* 3.8 21.5 - - + +
446B MET* 4.0 32.5 - - + -
447B PRO 5.5 0.2 - - - +
448B ARG* 5.7 6.5 - - - +
450B ASN* 3.2 30.3 + - + +
451B LEU 3.1 0.4 - - - -
452B LEU* 1.3 76.7 - - - +
454B GLU* 1.3 58.4 + - - +
456B LEU* 4.0 14.8 - - + -
457B GLN* 2.9 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ARG* 5.0 10.0 + - - +
449B ASN 5.7 0.9 - - - +
450B ASN 3.4 14.5 + - - +
451B LEU* 3.2 16.3 + - + +
453B ILE* 1.3 80.7 - - - +
455B MET* 1.3 64.7 + - + +
457B GLN* 3.4 10.6 + - - -
458B ALA* 3.5 12.1 + - - +
741Q GLU 5.3 4.7 - - - +
742Q ASN* 4.7 17.7 + - - +
743Q ALA 5.7 0.7 + - - -
744Q LEU* 4.6 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 3.9 27.6 - - + -
298B LEU 3.7 25.4 - - - +
299B GLN* 3.9 20.5 - - + +
302B TRP* 3.5 44.9 + - + -
451B LEU* 2.9 21.8 + - + +
452B LEU* 3.4 9.0 - - - +
454B GLU* 1.3 80.2 - - - +
456B LEU* 1.3 62.4 + - - +
457B GLN 3.4 0.2 + - - -
458B ALA* 3.4 16.0 + - - +
742Q ASN* 4.4 9.4 - - - +
745Q LEU* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TRP* 3.7 13.2 - - + +
434B LYS* 3.6 47.3 - - + +
437B LEU* 4.2 3.6 - - + -
438B TYR* 4.0 40.8 - - + +
441B HIS* 5.3 2.5 - - + -
452B LEU 2.7 20.4 + - - +
453B ILE* 3.2 22.4 + - + +
455B MET* 1.3 73.8 - - - +
457B GLN* 1.3 62.5 + - + +
458B ALA 3.3 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B TYR* 6.5 1.1 - - + -
441B HIS* 3.4 34.0 + - + +
448B ARG* 5.5 4.3 + - - -
453B ILE* 2.9 28.5 + - + +
454B GLU* 3.7 7.6 - - - +
455B MET 3.3 0.4 - - - -
456B LEU* 1.3 83.2 - - + +
458B ALA* 1.3 59.2 + - - +
----------------------------------------------------------
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