Contacts of the helix formed by residues 1426 - 1436 (chain A) in PDB entry 5UAK
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 SER1426 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1411A GLN 5.2 0.2 - - - -
1413A PHE* 3.8 16.2 - - - -
1424A TYR* 3.6 2.0 - - - +
1425A ASP* 1.3 82.6 - - - +
1427A ILE* 1.3 65.0 + - - +
1428A GLN* 3.9 10.5 + - - +
1429A LYS* 3.3 24.6 + - - +
1430A LEU* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1404A ILE* 4.5 27.4 - - + +
1407A MET 4.7 2.9 - - - +
1408A LEU* 5.3 13.5 - - + +
1413A PHE* 3.4 35.3 - - + -
1426A SER* 1.3 74.8 - - - +
1428A GLN* 1.3 60.2 + - + +
1430A LEU* 3.2 4.6 + - + +
1431A LEU* 2.8 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426A SER* 3.3 9.5 + - - +
1427A ILE* 1.3 79.7 - - + +
1429A LYS* 1.3 58.6 - - + +
1431A LEU* 5.3 1.1 - - - -
1432A ASN* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424A TYR* 3.8 14.8 - - + -
1425A ASP* 4.1 25.8 + - + +
1426A SER* 3.3 31.1 + - - +
1427A ILE 3.2 0.4 - - - -
1428A GLN* 1.3 80.2 - - + +
1430A LEU* 1.3 59.3 + - - +
1432A ASN* 2.9 14.8 - - - +
1433A GLU* 3.3 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243A LEU* 3.4 33.4 - - + -
1404A ILE* 4.7 7.6 - - + -
1413A PHE* 4.4 17.0 - - + -
1415A VAL* 3.4 33.9 - - + -
1424A TYR* 3.6 22.0 - - + -
1426A SER 3.2 10.4 + - - +
1427A ILE* 3.2 6.1 + - + +
1429A LYS* 1.3 78.9 - - - +
1431A LEU* 1.3 68.9 - - - +
1432A ASN 3.3 0.2 - - - -
1433A GLU* 3.0 13.6 + - + +
1434A ARG* 3.2 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1404A ILE* 5.1 21.3 - - + -
1405A GLU* 5.5 6.5 - - - +
1427A ILE* 2.8 43.7 + - + +
1428A GLN* 5.3 0.9 - - - -
1430A LEU* 1.3 76.3 - - - +
1432A ASN* 1.3 56.3 + - - +
1434A ARG* 5.1 0.4 - - - +
1435A SER* 3.1 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427A ILE 4.4 1.0 + - - -
1428A GLN* 2.9 28.3 + - - +
1429A LYS 2.9 11.1 - - - +
1431A LEU* 1.3 78.7 - - - +
1433A GLU* 1.3 77.7 + - - +
1436A LEU* 2.8 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1422A ARG* 5.0 6.2 + - - -
1424A TYR* 2.7 38.8 + - + +
1429A LYS* 3.3 17.6 - - - +
1430A LEU* 3.0 4.6 + - + +
1432A ASN* 1.3 86.0 + - - +
1434A ARG* 1.3 61.8 + - - +
1436A LEU 3.9 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1415A VAL* 6.2 3.6 - - - -
1430A LEU* 3.2 25.4 + - + +
1431A LEU* 5.1 0.9 - - - +
1433A GLU* 1.3 76.9 - - - +
1435A SER* 1.3 80.2 + - - +
1436A LEU 4.9 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431A LEU* 3.1 27.0 + - - -
1434A ARG* 1.3 96.3 + - - +
1436A LEU* 1.3 72.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1432A ASN* 2.8 44.3 + - + +
1433A GLU* 3.9 10.5 - - - -
1434A ARG 4.9 0.2 - - - -
1435A SER* 1.3 85.9 - - - +
----------------------------------------------------------
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