Contacts of the helix formed by residues 21 - 40 (chain A) in PDB entry 1S4X
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 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 1.3 59.0 + - - +
23A LEU 3.4 2.0 - - - -
24A ILE* 3.3 36.4 - - + +
25A THR* 2.4 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 1.3 82.0 - - - +
23A LEU* 1.3 66.6 + - + +
25A THR* 3.6 3.4 - - - -
26A ILE* 3.1 45.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
22A LEU* 1.3 82.3 - - + +
24A ILE* 1.3 61.8 + - + +
25A THR 2.7 6.4 + - - -
26A ILE* 3.9 18.6 - - + +
27A HIS* 2.4 61.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 3.3 40.2 - - + +
23A LEU* 1.3 78.2 - - + +
25A THR* 1.3 56.6 + - - +
27A HIS* 4.6 2.0 - - - -
28A ASP* 2.8 38.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 2.4 60.9 + - - +
22A LEU* 3.6 4.7 - - - -
23A LEU 2.7 0.2 + - - -
24A ILE* 1.3 76.8 - - - +
26A ILE* 1.3 62.9 + - + +
28A ASP* 3.8 1.8 - - - -
29A ARG* 2.8 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.1 39.2 + - + +
23A LEU* 2.8 19.8 + - + +
25A THR* 1.3 75.9 - - + +
27A HIS* 1.3 64.9 + - + +
28A ASP 3.0 5.8 + - - -
29A ARG* 3.4 51.9 + - - +
30A LYS* 3.7 8.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
23A LEU* 2.4 51.1 + - + +
24A ILE* 4.6 1.1 - - - -
26A ILE* 1.3 76.7 - - + +
28A ASP* 1.3 64.9 + - - +
30A LYS* 4.2 10.8 - - - +
31A GLU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 2.8 33.9 + - - +
25A THR* 3.6 1.7 + - - +
26A ILE 3.0 0.4 - - - -
27A HIS* 1.3 91.6 + - - +
29A ARG* 1.3 54.4 + - - +
30A LYS* 2.5 18.4 + - - +
31A GLU* 2.9 25.1 + - + +
32A PHE* 4.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 2.8 29.8 + - + +
26A ILE* 3.4 47.1 + - - +
28A ASP* 1.3 75.4 - - - +
30A LYS* 1.3 56.6 + - - +
31A GLU 3.1 0.2 - - - -
32A PHE* 2.8 17.6 + - + -
33A ALA* 2.4 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE 3.7 6.8 + - - +
27A HIS* 4.2 13.5 - - - +
28A ASP 2.5 6.8 + - - +
29A ARG* 1.3 78.0 - - - +
31A GLU* 1.3 60.7 + - - +
33A ALA* 3.1 12.8 + - + +
34A LYS* 2.6 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS 5.9 0.2 - - - +
28A ASP* 2.9 13.4 + - + +
30A LYS* 1.3 86.5 - - + +
32A PHE* 1.3 52.6 + - + +
34A LYS* 2.7 10.1 + - - +
35A PHE* 2.5 63.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP 4.0 0.8 + - - -
29A ARG* 2.8 22.4 + - + +
31A GLU* 1.3 76.9 - - + +
33A ALA* 1.3 66.1 + - - +
35A PHE* 3.6 8.9 - + + +
36A GLU* 2.8 26.7 + - - +
39A ARG* 5.1 17.3 - - - -
42A ALA* 4.6 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 2.4 33.6 + - + +
30A LYS* 3.4 16.2 - - + +
32A PHE* 1.3 73.1 - - - +
34A LYS* 1.3 55.8 + - - +
36A GLU* 2.6 40.7 - - - +
43A LYS* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS* 2.6 23.7 + - + +
31A GLU* 2.7 16.2 + - - +
33A ALA* 1.3 73.7 - - - +
35A PHE* 1.3 64.0 + - + +
36A GLU* 2.5 16.9 + - - +
37A GLU* 3.0 35.9 + - + +
38A GLU* 5.8 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 2.5 56.8 + - + +
32A PHE* 4.0 8.7 - + + +
34A LYS* 1.3 80.3 - - + +
36A GLU* 1.3 64.0 + - - +
37A GLU 3.1 0.7 - - - -
38A GLU* 2.8 48.9 + - - +
39A ARG* 3.3 16.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 2.8 11.8 + - - +
33A ALA* 2.6 38.6 - - - +
34A LYS 2.5 6.6 + - - +
35A PHE* 1.3 73.1 - - - +
37A GLU* 1.3 75.4 + - + +
38A GLU 2.7 0.2 + - - -
39A ARG* 4.7 0.9 - - - -
40A ALA* 2.3 48.6 + - + +
43A LYS* 3.1 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.0 28.2 + - + +
36A GLU* 1.3 87.9 - - + +
38A GLU* 1.3 63.9 + - + +
40A ALA* 4.6 3.1 + - - +
41A ARG* 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 5.8 4.3 + - - +
35A PHE* 2.8 39.6 + - - +
36A GLU 2.7 4.2 + - - -
37A GLU* 1.3 80.2 - - + +
39A ARG* 1.3 55.6 + - + +
40A ALA 3.5 0.2 - - - -
41A ARG* 2.4 32.2 + - - -
51A LEU* 3.6 7.4 - - - +
55A ALA* 4.0 29.4 - - + +
58A THR* 4.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 5.1 17.5 - - - -
35A PHE* 3.9 19.1 - - + +
36A GLU* 3.2 1.1 + - - -
38A GLU* 1.3 77.1 - - + +
40A ALA* 1.3 48.9 - - - +
41A ARG* 1.8 45.0 + - - +
42A ALA* 2.9 26.2 + - - +
46A THR* 4.4 8.9 + - - +
52A TYR* 3.7 46.1 + - + -
55A ALA* 4.0 17.6 - - + +
56A THR* 5.3 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 2.3 54.8 + - + +
37A GLU* 4.6 2.9 - - - +
38A GLU 3.5 1.0 - - - -
39A ARG* 1.3 59.1 - - - +
41A ARG* 1.3 54.3 + - + +
42A ALA* 3.3 2.2 - - - +
43A LYS* 2.8 22.5 - - + +
44A TRP* 2.6 38.8 + - + +
----------------------------------------------------------
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