Contacts of the helix formed by residues 4 - 23 (chain A) in PDB entry 1AX8
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 GLN 4 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 1.3 83.6 - - + +
5A LYS* 1.3 77.2 + - + +
7A GLN* 3.2 25.7 + - - +
8A ASP* 2.8 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE 3.3 3.3 - - - +
4A GLN* 1.3 90.7 - - + +
6A VAL* 1.3 60.7 - - + +
8A ASP* 3.5 20.8 + - - +
9A ASP* 2.9 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.3 25.1 - - - +
5A LYS* 1.3 77.0 - - + +
7A GLN* 1.3 55.2 + - - +
9A ASP* 3.2 7.7 + - - +
10A THR* 2.7 38.6 + - - +
86A LEU* 3.7 31.0 - - + +
89A VAL* 3.9 23.8 - - + +
90A LEU* 4.0 24.0 - - + +
93A SER* 5.3 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.0 36.8 + - + +
4A GLN* 3.3 33.3 - - - +
6A VAL* 1.3 74.1 - - - +
8A ASP* 1.3 58.8 + - - +
10A THR* 3.2 7.8 + - - -
11A LYS* 2.9 36.4 + - - +
90A LEU* 4.8 19.4 - - + +
140A LEU* 3.6 26.4 + - + -
141A ASP* 5.4 1.6 - - - +
143A SER* 3.7 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 2.8 45.3 + - - +
5A LYS* 3.5 30.1 + - - +
6A VAL 3.3 0.2 - - - -
7A GLN* 1.3 71.4 - - - +
9A ASP* 1.3 60.9 + - - +
11A LYS* 3.5 8.8 + - - +
12A THR* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 2.9 24.8 + - - +
6A VAL* 3.5 6.4 - - - +
8A ASP* 1.3 81.2 - - - +
10A THR* 1.3 59.7 + - - +
12A THR* 3.9 5.6 + - - -
13A LEU* 3.2 23.9 + - - +
86A LEU* 3.5 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 2.7 29.3 + - - +
7A GLN* 3.2 8.9 + - - -
9A ASP* 1.3 75.2 - - - +
11A LYS* 1.3 63.6 + - - +
13A LEU* 3.2 3.3 + - - +
14A ILE* 3.0 28.7 + - + +
83A LEU* 3.5 23.7 - - + +
86A LEU* 3.6 24.7 + - + +
87A LEU* 4.5 12.3 - - + -
90A LEU* 5.7 4.0 - - + +
140A LEU* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN* 2.9 18.3 + - - +
8A ASP* 3.8 9.0 - - - +
10A THR* 1.3 75.0 - - - +
12A THR* 1.3 62.3 + - - +
14A ILE* 3.4 6.6 + - - +
15A LYS* 3.1 51.9 + - - +
137A LEU* 3.2 38.9 + - + +
140A LEU* 5.3 5.7 - - + +
141A ASP* 2.7 37.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP 2.9 21.8 + - - -
9A ASP* 3.9 7.5 + - - +
11A LYS* 1.3 73.2 - - - +
13A LEU* 1.3 66.8 + - - +
15A LYS* 3.2 17.8 + - - +
16A THR* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 3.2 16.0 + - - +
10A THR 3.2 4.0 + - - +
12A THR* 1.3 81.5 - - - +
14A ILE* 1.3 62.7 + - - +
16A THR* 3.2 15.4 - - + -
17A ILE* 3.1 39.7 + - + +
79A ASP* 3.8 24.0 - - - +
82A ASN* 3.6 21.1 - - + +
83A LEU* 3.5 39.3 - - + +
86A LEU* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.0 24.8 + - + +
11A LYS* 3.7 6.7 - - - +
12A THR 3.2 0.2 - - - -
13A LEU* 1.3 73.9 - - - +
15A LYS* 1.3 66.2 + - - +
17A ILE* 3.1 9.5 + - - +
18A VAL* 2.9 30.5 + - + +
83A LEU* 3.7 26.9 - - + -
87A LEU* 6.3 0.2 - - + -
133A LEU* 3.5 32.5 - - + +
136A MET* 4.2 16.2 - - + -
137A LEU* 3.9 19.3 - - + +
140A LEU* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.1 52.6 + - - +
12A THR* 3.2 15.0 + - - +
14A ILE* 1.3 74.6 - - - +
16A THR* 1.3 57.0 + - - +
18A VAL* 3.2 7.2 + - - +
19A THR* 2.9 37.5 + - - +
137A LEU* 4.5 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.1 20.1 + - - +
13A LEU* 3.2 20.8 - - + +
15A LYS* 1.3 76.5 - - - +
17A ILE* 1.3 57.1 + - - +
19A THR* 3.4 6.9 + - - +
20A ARG* 2.8 55.8 + - - +
79A ASP* 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.1 24.6 + - + +
14A ILE* 3.1 4.5 + - - +
16A THR* 1.3 72.4 - - - +
18A VAL* 1.3 60.5 + - - +
20A ARG* 3.6 8.4 - - - +
21A ILE* 3.0 38.5 + - + +
76A ILE* 3.9 29.2 - - + -
79A ASP* 3.4 45.8 - - + +
80A LEU* 4.1 10.5 - - + -
83A LEU* 4.5 15.5 - - + -
133A LEU* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 2.9 27.6 + - + +
15A LYS* 3.6 7.9 - - - +
17A ILE* 1.3 76.1 - - - +
19A THR* 1.3 58.3 + - - +
21A ILE* 3.3 3.8 + - - -
22A ASN* 3.0 31.6 + - - +
130A GLN* 3.0 27.7 + - + +
133A LEU* 3.8 26.9 - - + -
134A GLN* 3.6 36.6 - - + +
137A LEU* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 2.9 21.4 + - - +
16A THR* 3.5 7.0 - - - +
18A VAL* 1.3 74.8 - - - +
20A ARG* 1.3 65.7 + - - +
22A ASN* 3.1 12.0 + - + +
23A ASP* 3.0 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 2.8 42.8 + - - +
17A ILE* 3.6 11.0 - - - +
18A VAL 3.3 0.2 - - - -
19A THR* 1.3 79.8 - - - +
21A ILE* 1.3 60.1 + - - +
23A ASP* 3.6 8.7 + - - +
24A ILE* 3.3 21.0 + - - +
72A ASN* 4.5 7.3 + - - +
75A GLN* 2.7 52.5 - - - +
76A ILE* 3.5 28.9 - - + -
79A ASP* 2.5 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.0 31.7 + - + +
18A VAL 3.6 4.9 - - - +
19A THR 3.1 0.2 - - - -
20A ARG* 1.3 75.1 - - - +
22A ASN* 1.3 67.3 + - - +
24A ILE* 3.2 23.2 + - + +
76A ILE* 3.7 19.3 - - + -
126A LEU* 3.6 39.5 - - + +
127A SER* 5.4 0.9 - - - -
129A LEU* 4.0 25.4 - - + -
130A GLN* 3.7 24.7 - - + +
133A LEU* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.0 28.1 + - - +
19A THR* 3.1 15.7 + - - +
21A ILE* 1.3 76.6 - - - +
23A ASP* 1.3 72.1 + - - +
24A ILE 2.8 8.0 + - - -
130A GLN* 2.8 23.7 + - - +
134A GLN* 5.7 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 3.0 31.7 + - - +
20A ARG* 3.8 8.2 - - - +
21A ILE 3.3 0.2 - - - -
22A ASN* 1.3 79.0 - - - +
24A ILE* 1.3 62.9 + - - +
72A ASN* 5.9 2.7 - - - +
----------------------------------------------------------
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