Contacts of the helix formed by residues 1 - 26 (chain B) 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 LYS 1 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B MET* 1.3 67.1 - - - +
2B ARG* 1.3 54.2 + - - +
3B GLU* 2.9 38.6 - - - +
4B SER* 3.1 21.4 + - - -
5B HIS* 2.7 34.5 + - + +
3D A 5.1 1.9 - - + +
4D G 2.8 53.9 + - + +
5D T 2.6 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 2 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B MET* 2.5 63.0 + - + +
1B LYS* 1.3 78.7 - - - +
3B GLU* 1.3 48.6 + - - +
5B HIS* 3.1 24.6 - - + +
6B LYS* 2.8 45.4 + - + +
9C T 5.0 8.1 - - - +
10C G 5.3 11.4 - - + +
11C G 2.9 42.0 + - - +
12C G 4.1 7.5 + - - -
5D T 5.0 13.1 + - - +
6D C 4.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B MET 3.1 24.1 + - - +
1B LYS* 3.1 33.0 - - - +
2B ARG* 1.3 78.1 - - - +
4B SER* 1.3 66.4 + - - +
6B LYS* 4.0 14.9 - - - +
7B HIS* 3.4 21.4 + - - -
4D G 5.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS* 3.1 41.6 + - - -
3B GLU* 1.3 81.1 - - - +
5B HIS* 1.3 52.5 + - - +
6B LYS 2.5 17.7 + - - -
7B HIS* 2.5 27.8 + - - +
8B ALA* 2.5 22.1 + - - +
5D T 4.2 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS* 2.7 22.3 + - + +
2B ARG* 3.1 30.7 + - + -
4B SER* 1.3 69.6 - - - +
6B LYS* 1.3 54.6 + - - +
8B ALA* 3.9 8.7 - - - -
9B GLU* 2.7 33.8 + - + +
9C T 3.2 45.6 - + + +
10C G 2.7 20.5 + - - -
11C G 2.5 39.2 + + - -
5D T 6.3 4.3 - - + -
6D C 5.0 0.7 - - - -
7D C 4.2 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ARG* 2.8 29.3 + - + +
3B GLU* 4.0 12.1 - - - +
4B SER 2.5 4.4 + - - -
5B HIS* 1.3 72.3 - - - +
7B HIS* 1.3 58.1 + - + +
8B ALA 2.6 15.0 + - - -
9B GLU 3.0 2.4 + - - -
10B GLN* 3.0 26.0 + - - +
8C G 2.5 74.1 + - + +
9C T 3.8 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU 3.4 22.3 + - - -
4B SER* 2.5 21.2 + - - +
6B LYS* 1.3 75.2 - - + +
8B ALA* 1.3 57.2 + - - +
10B GLN* 3.4 24.2 - - - +
11B ALA* 3.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER* 2.5 26.5 + - - +
5B HIS* 3.9 10.3 - - - +
6B LYS 2.6 1.0 + - - -
7B HIS* 1.3 68.0 - - - +
9B GLU* 1.3 53.3 + - - +
10B GLN 2.3 19.1 + - - -
11B ALA* 2.6 20.2 + - - +
12B ARG* 2.8 11.6 + - - -
5D T 6.0 1.3 - - - +
6D C 5.1 10.1 - - - +
7D C 6.0 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B HIS* 2.7 25.6 + - - +
6B LYS* 3.0 2.2 + - - -
8B ALA* 1.3 70.3 - - - +
10B GLN* 1.3 54.3 + - - +
12B ARG* 3.4 20.6 - - - +
13B ARG* 3.3 27.0 + - - +
9C T 4.3 12.9 - - + +
11C G 4.6 0.9 - - - +
7D C 2.9 55.5 - - + +
8D C 2.8 22.2 + - - +
9D A 2.7 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS 3.0 16.7 + - - +
7B HIS* 3.4 12.9 - - - +
8B ALA 2.3 11.9 + - - -
9B GLU* 1.3 68.9 - - - +
11B ALA* 1.3 70.2 + - - +
12B ARG 3.0 0.4 - - - -
13B ARG* 3.3 4.3 + - - +
14B ASN* 2.7 38.1 + - + +
7C C 4.1 35.4 + - + +
8C G 5.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B HIS 3.5 9.8 + - - +
8B ALA* 2.6 15.6 + - - +
10B GLN* 1.3 81.8 + - - +
12B ARG* 1.3 70.1 + - - +
14B ASN* 2.3 35.7 - - - +
15B ARG* 3.0 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 5.7 1.0 - - - +
8B ALA 2.8 13.2 + - - +
9B GLU* 3.4 26.2 - - + +
11B ALA* 1.3 83.0 - - - +
13B ARG* 1.3 55.2 + - - +
14B ASN 2.6 13.7 + - - -
15B ARG* 2.7 53.5 + - - +
16B LEU* 3.6 2.6 + - - +
6D C 2.8 31.2 + - - +
7D C 2.4 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.6 22.6 - - - +
9B GLU* 3.3 24.9 + - - +
10B GLN* 3.3 6.4 + - - +
12B ARG* 1.3 76.2 - - - +
14B ASN* 1.3 60.6 + - - +
16B LEU* 3.3 31.7 - - + +
17B ALA* 3.9 3.8 + - - +
42B LYS* 4.3 17.9 - - - +
6C A 4.5 9.6 + - + +
7C C 2.9 44.7 + - - +
8C G 3.2 22.6 + - - -
8D C 6.1 1.3 - - - -
9D A 4.3 15.8 + - - +
10D C 4.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 2.7 16.8 + - - +
11B ALA* 2.3 30.5 - - - +
12B ARG 2.6 4.9 + - - -
13B ARG* 1.3 71.5 - - - +
15B ARG* 1.3 65.4 + - - +
16B LEU 3.1 1.8 - - - -
17B ALA* 2.6 35.3 + - - +
18B VAL* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 6.1 1.4 - - - +
43A ALA* 5.3 5.8 - - + +
44A THR* 3.8 17.8 - - - +
47A GLU* 3.5 32.7 + - + +
11B ALA 4.0 2.0 - - - +
12B ARG* 2.7 64.1 + - - +
14B ASN* 1.3 78.4 + - - +
16B LEU* 1.3 54.7 + - - +
17B ALA 2.5 17.8 + - - -
18B VAL* 3.0 26.3 + - + +
19B ALA* 3.3 11.3 + - + +
7D C 2.6 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.8 15.5 - - + -
20A LEU* 4.6 3.8 - - + -
42A LYS 3.3 11.4 - - - +
43A ALA* 3.1 48.2 - - + +
46A VAL* 3.9 17.5 - - + -
12B ARG 3.6 1.4 + - - +
13B ARG* 3.3 30.9 + - + +
15B ARG* 1.3 78.1 - - - +
17B ALA* 1.3 55.4 + - - +
19B ALA* 5.5 0.4 - - - -
20B LEU* 2.9 29.4 + - + +
42B LYS* 4.7 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG 4.6 2.7 - - - +
14B ASN* 2.6 23.6 + - - +
15B ARG 2.5 8.1 + - - -
16B LEU* 1.3 71.1 - - - +
18B VAL* 1.3 56.6 + - - +
19B ALA 3.0 2.4 + - - -
20B LEU* 3.1 6.8 + - + -
21B HIS* 2.4 41.0 + - + +
42B LYS* 6.5 0.7 - - + -
6C A 5.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 3.1 24.4 + - - +
15B ARG* 3.0 31.4 - - + +
17B ALA* 1.3 72.4 - - - +
19B ALA* 1.3 51.2 + - + +
21B HIS* 2.7 33.2 + - - +
22B GLU* 2.8 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.9 15.7 - - + +
47A GLU* 4.2 32.1 - - + +
50A CYS* 6.4 1.8 - - + -
15B ARG* 3.3 12.6 + - + +
16B LEU 5.0 0.2 - - - +
17B ALA 3.0 0.4 + - - -
18B VAL* 1.3 75.0 - - + +
20B LEU* 1.3 56.1 + - - +
21B HIS 2.8 3.4 - - - -
22B GLU* 2.3 39.6 + - - -
23B LEU* 3.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.7 0.9 - - + -
20A LEU* 4.5 4.9 - - + -
46A VAL* 3.1 34.4 - - + +
16B LEU* 2.9 26.0 + - + +
17B ALA* 3.1 7.7 + - - +
19B ALA* 1.3 75.4 - - - +
21B HIS* 1.3 64.7 + - - +
23B LEU* 3.3 18.3 + - + +
24B ALA 3.9 2.9 + - - -
41B SER 3.1 27.8 - - - +
42B LYS* 3.1 24.7 - - + -
45B THR* 4.6 8.5 - - + +
46B VAL* 3.2 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 2.4 30.1 + - + +
18B VAL* 2.7 23.0 + - + +
19B ALA 2.6 1.6 + - - -
20B LEU* 1.3 75.6 - - - +
22B GLU* 1.3 72.5 + - + +
23B LEU 2.8 11.6 + - - -
24B ALA* 3.5 3.5 + - - +
25B SER* 3.0 30.1 + - - -
41B SER 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 3.5 26.3 - - - -
54A ARG* 3.9 20.3 + - - -
18B VAL 2.8 13.9 + - - +
19B ALA* 2.3 23.2 + - - +
21B HIS* 1.3 84.1 - - + +
23B LEU* 1.3 54.2 + - - +
25B SER* 2.5 21.8 + - - +
26B LEU* 3.3 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 29.4 - - + -
46A VAL* 4.2 11.2 - - + +
49A ALA* 3.9 5.4 - - + +
50A CYS* 3.4 47.6 - - + +
53A ILE* 4.7 13.5 - - + +
19B ALA 3.0 4.2 + - - +
20B LEU* 3.5 17.0 - - + +
21B HIS 2.8 3.8 + - - -
22B GLU* 1.3 78.8 - - - +
24B ALA* 1.3 66.1 + - - +
25B SER* 2.9 1.3 + - - -
26B LEU* 2.8 15.2 + - - +
27B ILE* 2.8 13.2 + - + -
45B THR* 5.6 1.1 - - + -
46B VAL* 5.3 1.3 - - + -
49B ALA* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 3.9 1.0 + - - -
21B HIS 3.5 5.0 + - - +
23B LEU* 1.3 73.5 - - - +
25B SER* 1.3 52.8 - - - +
26B LEU* 2.5 18.3 + - - -
27B ILE* 2.7 29.2 + - + +
32B LYS* 3.4 30.3 + - - +
45B THR* 3.3 33.1 - - + +
49B ALA* 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS* 3.0 21.5 + - - -
22B GLU* 2.5 57.0 + - - -
24B ALA* 1.3 73.4 - - - +
26B LEU* 1.3 92.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 5.1 4.7 - - - +
54A ARG* 5.0 20.2 - - - +
57A GLN* 4.8 2.2 + - - +
22B GLU* 3.3 26.5 - - + +
23B LEU 2.8 4.4 + - - +
24B ALA 2.5 3.8 + - - -
25B SER* 1.3 104.1 + - - +
27B ILE* 1.3 60.5 + - - +
28B PRO* 2.7 21.2 - - - +
----------------------------------------------------------
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