Contacts of the helix formed by residues 444 - 454 (chain D) in PDB entry 1ZQ1
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 PRO 444 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D ARG* 3.2 20.4 - - + +
443D ILE* 1.3 85.9 - - - +
445D ASP* 1.3 63.9 + - - +
446D ASP* 2.8 22.4 - - + -
447D LEU* 2.9 22.4 + - + +
448D LYS* 2.8 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.9 5.0 - - - +
62B GLU* 5.6 2.1 - - - +
63B LYS* 2.7 39.1 + - - -
442D ARG* 5.4 5.5 + - - -
443D ILE 3.6 1.3 + - - +
444D PRO* 1.3 71.2 - - - +
446D ASP* 1.3 54.6 + - - +
448D LYS* 3.4 14.3 + - - +
449D LYS* 2.8 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D PRO* 3.7 14.1 - - + -
445D ASP* 1.3 80.4 - - - +
447D LEU* 1.3 66.5 + - - +
449D LYS* 3.4 4.8 + - - +
450D LYS* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 5.8 4.5 - - + -
102D GLU* 3.9 22.2 - - + +
105D LEU* 4.0 21.5 - - + -
443D ILE* 4.5 8.3 - - + -
444D PRO* 2.9 23.7 + - + +
446D ASP* 1.3 82.1 + - - +
448D LYS* 1.3 66.8 + - - +
450D LYS* 3.4 8.6 + - + -
451D ILE* 3.1 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.1 35.1 + - - +
63B LYS* 3.6 3.2 - - - +
105D LEU* 5.4 1.8 - - + -
109D TYR* 3.3 25.0 + - + +
115D PRO* 3.8 13.9 + - + -
116D VAL 3.6 19.8 + - - -
117D ASP* 2.7 29.9 + - - +
443D ILE* 3.5 31.8 + - + +
444D PRO 2.8 13.3 + - - +
445D ASP* 3.1 16.8 + - - +
447D LEU* 1.3 76.8 - - - +
449D LYS* 1.3 55.3 + - - +
451D ILE* 3.4 2.1 + - - -
452D LYS* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 5.8 3.1 - - - +
445D ASP 2.8 20.5 + - - +
446D ASP* 3.7 5.2 - - - +
448D LYS* 1.3 70.2 - - - +
450D LYS* 1.3 66.9 + - - +
452D LYS* 3.0 18.0 + - - -
453D GLU* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D ASP* 3.3 12.8 + - - +
447D LEU* 3.8 14.6 - - + +
449D LYS* 1.3 79.7 - - - +
451D ILE* 1.3 63.3 + - + +
453D GLU* 4.1 8.6 + - - +
454D ASN* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLU* 4.2 19.5 - - + +
105D LEU* 3.6 33.7 - - + -
106D GLN* 3.8 38.3 - - + +
109D TYR* 4.2 9.6 - - + -
447D LEU* 3.1 35.7 + - + +
448D LYS* 3.9 2.9 - - - +
450D LYS* 1.3 75.0 - - + +
452D LYS* 1.3 61.7 + - - +
453D GLU 3.2 3.2 + - - -
454D ASN* 3.8 3.3 + - - +
455D LEU* 2.8 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 3.6 39.6 + - + +
27B GLU* 5.0 10.3 - - - +
109D TYR* 3.6 39.1 - - + +
448D LYS 2.9 20.3 + - - +
449D LYS* 3.0 7.6 + - - +
451D ILE* 1.3 75.8 - - - +
453D GLU* 1.3 61.0 + - + +
455D LEU* 3.1 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D LYS* 3.1 24.9 + - + +
450D LYS* 4.1 10.4 - - - +
452D LYS* 1.3 79.4 - - + +
454D ASN* 1.3 62.1 + - - +
455D LEU* 2.7 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 454 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLN* 4.7 3.4 - - - +
450D LYS* 2.9 30.5 + - - +
451D ILE* 3.8 5.1 + - - +
453D GLU* 1.3 79.7 + - - +
455D LEU* 1.3 65.2 + - - +
456D PRO* 3.4 7.1 - - - +
----------------------------------------------------------
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