Contacts of the helix formed by residues 19 - 29 (chain A) in PDB entry 1IXB
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 ASP 19 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.4 10.8 - - - +
17A HIS 4.2 1.2 + - - -
18A PHE* 1.3 74.5 - - - +
20A LYS* 1.3 60.8 + - - +
21A GLN* 4.0 4.8 + - + +
22A THR* 2.6 42.7 + - - +
23A MET* 3.0 26.8 + - - +
172A ALA 5.1 2.8 - - - +
173A TYR* 5.7 1.2 - - - -
175A LEU* 4.0 10.6 - - - +
176A LYS* 3.6 37.6 + - + +
177A PHE* 4.9 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.5 28.5 - - + +
12A ASP* 3.7 28.5 + - + +
15A GLU* 2.8 22.6 + - + +
18A PHE 3.6 1.0 + - - -
19A ASP* 1.3 69.8 - - - +
21A GLN* 1.3 70.2 + - + +
23A MET* 3.7 1.6 - - - +
24A GLU* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 3.3 8.1 + - + +
20A LYS* 1.3 82.7 - - + +
22A THR* 1.3 62.5 + - - +
24A GLU* 3.3 19.0 + - - +
25A ILE* 3.1 41.0 + - + +
175A LEU* 4.0 17.7 - - + -
178B GLN* 5.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 2.6 37.0 + - - +
21A GLN* 1.3 74.7 - - - +
23A MET* 1.4 70.2 + - - +
25A ILE* 4.5 4.9 - - + +
26A HIS* 2.8 37.9 + - + +
171A HIS 3.6 23.5 + - - +
172A ALA* 3.7 20.4 - - - +
173A TYR 5.7 0.5 - - - -
175A LEU* 3.5 24.5 + - - +
174B PHE* 5.4 2.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 5.1 3.8 - - + +
9A TYR* 3.7 25.8 - - + +
11A TYR* 3.4 35.4 - - + +
14A LEU* 3.7 32.1 - - + -
18A PHE* 4.3 21.5 - - + +
19A ASP 3.0 21.0 + - - +
20A LYS 3.7 2.2 - - - +
21A GLN 3.3 0.4 - - - -
22A THR* 1.4 75.7 - - - +
24A GLU* 1.3 63.8 + - - +
26A HIS* 3.7 6.8 - - - +
27A HIS* 3.1 26.0 + - - +
84A PHE* 5.8 1.6 - - - -
85A TRP* 3.8 30.3 - - + -
88A LEU* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.6 42.0 - - + +
20A LYS 3.1 15.2 + - - +
21A GLN* 3.8 18.4 + - - +
23A MET* 1.3 78.0 - - - +
25A ILE* 1.3 58.3 + - + +
28A THR* 2.8 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.1 43.4 + - + +
22A THR* 3.9 4.0 - - + +
24A GLU* 1.3 77.0 - - + +
26A HIS* 1.3 59.7 + - - +
28A THR* 4.0 5.6 - - - -
29A LYS* 2.8 54.1 + - + +
30A HIS* 3.3 25.6 + - + -
175A LEU* 4.1 15.9 - - + -
174B PHE* 4.4 14.1 - - + -
178B GLN* 3.4 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 2.8 32.6 + - + +
23A MET* 3.7 6.2 - - - +
25A ILE* 1.3 74.3 - - - +
27A HIS* 1.3 56.7 + - - +
30A HIS* 3.5 11.6 + - + -
31A HIS* 2.9 28.1 + - - +
81A HIS* 3.1 12.8 + + - -
84A PHE* 4.0 17.8 - + - -
85A TRP* 3.5 17.9 - + + -
167A ASP* 3.0 16.2 - - - -
171A HIS* 3.1 15.4 + + + +
172A ALA* 3.9 21.6 - - + -
206A MH2 2.2 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.4 40.1 - - + +
5A PRO 2.8 28.4 + - - -
6A SER* 5.1 1.6 - - - -
7A LEU* 3.6 30.7 - - + +
11A TYR* 2.8 33.0 + + + -
23A MET 3.1 17.6 + - - +
26A HIS* 1.3 77.1 - - - +
28A THR* 1.3 64.3 + - + +
31A HIS* 3.4 1.7 - - - +
32A GLN 3.3 20.1 + - - -
85A TRP* 3.8 22.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.3 8.5 - - + -
11A TYR* 3.2 29.4 - - + +
24A GLU* 2.8 36.7 + - + +
25A ILE* 4.0 1.0 - - - -
27A HIS* 1.3 76.3 - - + +
29A LYS* 1.3 71.7 + - - +
32A GLN* 3.2 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 2.8 29.3 + - + +
28A THR* 1.3 92.1 - - - +
30A HIS* 1.3 71.3 + - + +
31A HIS 3.5 0.4 - - - -
32A GLN* 3.4 2.0 + - - +
33A THR* 2.9 29.8 + - - -
178B GLN* 3.1 34.3 - - + +
179B ASN* 4.3 9.4 - - + -
180B ARG* 5.9 5.7 - - - +
----------------------------------------------------------
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