Contacts of the helix formed by residues 9 - 26 (chain A) in PDB entry 1A0A
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 GLU 9 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS* 5.6 1.1 - - + -
6A LYS 2.7 15.0 + - - +
7A HIS 2.9 0.2 - - - -
8A ALA* 1.3 75.1 - - - +
10A GLN* 1.3 55.9 + - + +
12A ARG* 2.5 33.1 + - - +
13A ARG* 2.5 59.5 + - - +
4C A 5.6 1.6 - - - +
5C C 2.8 34.7 + - - -
6C A 2.6 21.6 + - - +
10D C 6.4 0.4 - - + -
11D G 4.5 3.6 - - + +
12D T 3.3 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS 4.3 0.4 + - - -
7A HIS* 3.5 4.4 + - - +
9A GLU* 1.3 74.6 - - + +
11A ALA* 1.3 53.7 + - - +
12A ARG 2.6 7.8 + - - -
13A ARG* 2.6 36.4 + - - +
14A ASN* 2.5 47.6 + - + +
17A ALA* 5.3 6.3 - - - +
9D A 4.5 8.1 + - - +
10D C 2.9 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS* 2.8 54.5 + - + +
8A ALA* 5.1 0.4 - - - -
10A GLN* 1.3 71.4 - - - +
12A ARG* 1.3 55.3 + - - +
14A ASN* 2.9 22.7 + - - +
15A ARG* 4.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA 2.9 21.7 + - - +
9A GLU* 2.5 64.3 + - - +
10A GLN 2.6 3.4 + - - -
11A ALA* 1.3 75.8 - - - +
13A ARG* 1.3 76.1 + - - +
14A ASN* 3.2 9.0 - - - +
15A ARG* 3.4 22.3 + - - +
16A LEU* 4.2 1.0 + - - +
42B LYS* 5.7 4.0 - - - +
43B ALA* 5.0 2.4 - - - +
3C C 4.6 4.9 - - - -
4C A 2.7 52.0 + - - +
5C C 2.9 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 2.5 44.6 + - - +
10A GLN* 2.6 43.1 + - - +
12A ARG* 1.3 76.8 - - - +
14A ASN* 1.3 52.7 + - - -
15A ARG 3.1 2.7 - - - -
16A LEU* 2.7 40.8 + - + +
17A ALA* 3.0 9.7 + - + +
13B ARG* 3.6 35.4 - - - +
42B LYS* 5.9 0.8 - - - +
6C A 4.3 1.4 + - - +
7C C 5.0 0.4 - - - +
9D A 4.8 6.5 - - - +
10D C 3.6 34.8 + - - +
11D G 3.5 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 2.5 26.4 + - + +
11A ALA* 2.9 28.3 + - - +
12A ARG 3.2 2.1 - - - +
13A ARG* 1.3 70.4 - - - +
15A ARG* 1.3 99.0 + - - +
17A ALA* 2.9 24.1 - - - +
18A VAL* 3.1 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 4.0 7.3 + - - -
12A ARG* 3.6 14.4 + - - +
13A ARG 2.9 0.6 + - - -
14A ASN* 1.3 107.8 + - - +
16A LEU* 1.3 66.5 + - - +
17A ALA 2.7 2.1 + - - -
18A VAL* 2.8 13.0 + - + +
19A ALA* 2.7 23.0 + - - +
43B ALA* 3.8 7.2 - - + -
44B THR* 6.0 2.2 - - - -
47B GLU* 3.3 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG 5.3 0.2 - - - +
13A ARG* 2.7 26.2 + - + +
15A ARG* 1.3 74.8 - - - +
17A ALA* 1.3 66.0 + - - +
19A ALA* 3.8 1.1 - - + -
20A LEU* 3.1 27.9 + - + +
42A LYS* 6.1 1.6 - - + +
16B LEU* 4.8 11.7 - - + -
20B LEU* 4.7 0.4 - - + -
42B LYS* 3.2 42.4 - - + -
43B ALA* 2.9 36.4 - - + +
46B VAL* 3.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 5.3 7.0 - - - +
13A ARG* 3.0 7.8 + - + +
14A ASN* 2.9 21.7 + - - +
15A ARG 2.7 4.6 + - - -
16A LEU* 1.3 75.3 - - - +
18A VAL* 1.3 55.4 - - + +
20A LEU* 2.8 29.4 - - - +
21A HIS* 2.9 13.5 + - + +
42A LYS* 4.7 17.8 - - + +
9D A 5.6 3.6 - - - +
----------------------------------------------------------
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 ASN* 3.1 20.4 - - + +
15A ARG* 2.8 9.2 + - + +
17A ALA* 1.3 69.5 - - + +
19A ALA* 1.3 59.9 + - - +
21A HIS* 2.5 23.1 + - + +
22A GLU* 2.4 54.8 + - + +
47B GLU* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG 2.7 20.3 + - - +
16A LEU* 3.5 10.5 - - - +
18A VAL* 1.3 76.7 - - - +
20A LEU* 1.3 64.6 + - - +
22A GLU* 4.5 3.1 - - - +
23A LEU* 2.9 21.1 + - - +
43B ALA* 3.4 14.4 - - - +
46B VAL* 3.1 39.2 - - + +
47B GLU* 4.2 8.3 - - + +
50B CYS* 3.7 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.1 27.8 + - + +
17A ALA 2.8 15.8 + - - +
19A ALA* 1.3 80.1 - - - +
21A HIS* 1.3 56.4 + - + +
23A LEU* 2.9 27.1 - - + +
24A ALA* 3.1 10.4 + - - +
42A LYS* 3.9 34.5 - - + +
45A THR* 3.6 23.8 + - - +
46A VAL* 3.1 40.4 - - + +
16B LEU* 4.6 6.7 - - + -
20B LEU* 4.5 3.8 - - + -
46B VAL* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 2.9 10.6 + - + -
18A VAL* 2.5 36.8 + - + +
20A LEU* 1.3 71.6 - - + +
22A GLU* 1.3 51.6 + - + +
23A LEU 2.9 5.6 - - - -
24A ALA* 2.6 36.3 + - + +
25A SER* 2.9 7.8 + - - -
42A LYS* 3.7 32.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.4 39.7 + - + +
19A ALA* 4.7 2.0 - - - +
21A HIS* 1.3 65.0 - - + +
23A LEU* 1.3 60.4 + - - +
24A ALA 2.9 4.5 - - - -
25A SER* 2.8 29.2 + - - +
26A LEU* 3.3 12.0 + - - +
47B GLU* 5.9 4.7 - - - +
50B CYS* 2.9 22.0 - - + +
53B ILE* 5.6 0.2 - - - +
54B ARG* 5.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.9 7.6 + - - +
20A LEU* 2.9 21.5 - - + +
22A GLU* 1.3 76.8 - - - +
24A ALA* 1.3 50.1 + - - +
26A LEU 4.7 1.2 - - - -
27A ILE* 2.6 28.2 + - - +
45A THR 5.2 1.3 - - - +
46A VAL* 4.2 22.2 - - + -
49A ALA* 3.4 36.9 - - + +
23B LEU* 4.0 19.3 - - + -
46B VAL* 3.5 21.5 - - + -
49B ALA* 4.2 5.6 - - + +
50B CYS* 2.6 27.2 - - - +
53B ILE* 4.0 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU 3.1 7.5 + - - +
21A HIS* 2.6 27.3 + - + +
23A LEU* 1.3 77.4 - - - +
25A SER* 1.3 55.6 + - - -
27A ILE* 2.7 32.5 + - + +
45A THR* 5.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS 2.9 5.9 + - - -
22A GLU* 2.8 34.8 + - - +
24A ALA* 1.3 79.8 - - - +
26A LEU* 1.3 72.7 + - - +
27A ILE 3.3 6.9 + - - +
54B ARG* 5.1 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU 3.3 10.3 + - - +
23A LEU 4.8 1.3 - - - -
25A SER* 1.3 93.4 - - - +
27A ILE* 1.3 52.5 + - - +
52A TYR* 2.6 31.3 - - - -
50B CYS* 5.3 2.9 - - + +
53B ILE* 3.9 19.3 - - + +
54B ARG* 3.1 54.5 - - - +
57B GLN* 2.9 42.0 - - + +
----------------------------------------------------------
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