Contacts of the helix formed by residues 4 - 21 (chain O) in PDB entry 1S72
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 ASN 4 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6560 G 2.7 24.8 + - - +
6570 G 3.5 7.5 + - - -
27C ARG* 3.1 34.8 + - - +
29C ASP* 3.9 4.7 - - - -
2O LYS* 4.8 1.9 - - - +
3O THR* 1.3 72.9 + - - +
5O PRO* 1.3 69.3 - - - +
6O ARG* 2.8 28.4 + - - +
7O LEU* 3.6 24.1 - - + +
8O SER* 3.1 21.0 + - - -
37O ARG* 6.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 5 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL 5.8 2.9 - - - +
27C ARG* 4.0 6.1 - - - -
28C SER* 4.3 18.8 - - - +
29C ASP* 3.1 24.0 - - + +
3O THR 3.1 9.2 - - - +
4O ASN* 1.3 89.0 - - - +
6O ARG* 1.3 57.4 + - + +
8O SER* 3.3 8.7 - - - -
9O SER* 3.0 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 6 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 3.5 41.2 - - - +
26C VAL 5.1 6.8 + - - +
27C ARG* 4.2 19.5 - - - +
4O ASN* 2.8 17.8 + - - +
5O PRO* 1.3 76.0 - - + +
7O LEU* 1.3 59.7 + - - +
8O SER 3.0 1.3 - - - -
9O SER* 3.0 7.4 + - - +
10O LEU* 2.8 30.5 + - - +
99O GLU* 5.3 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6560 G 4.0 18.8 - - - +
2O LYS* 4.0 31.4 - - + +
4O ASN* 3.4 23.3 + - + +
6O ARG* 1.3 79.2 - - - +
8O SER* 1.3 61.6 + - - +
10O LEU* 3.4 7.1 + - + +
11O ILE* 3.1 33.5 + - + +
33O LEU* 4.2 29.2 - - + -
37O ARG* 5.6 3.4 - - + +
40O HIS* 4.9 9.4 - - + -
79O VAL* 4.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 8 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O LYS* 5.1 11.5 - - - +
4O ASN 3.1 14.9 + - - -
5O PRO* 3.3 14.6 - - - -
7O LEU* 1.3 79.9 - - - +
9O SER* 1.3 60.3 + - - +
11O ILE* 3.3 11.2 + - - +
12O ALA* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O PRO 3.0 14.6 + - - -
6O ARG* 3.0 10.1 + - - -
8O SER* 1.3 72.3 - - - +
10O LEU* 1.3 66.4 + - - +
12O ALA* 3.2 7.2 + - - +
13O ASP* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O ARG 2.8 19.3 + - - +
7O LEU* 3.6 9.9 - - + +
9O SER* 1.3 71.1 - - - +
11O ILE* 1.3 59.2 + - - +
13O ASP* 3.0 8.1 + - + +
14O LEU* 2.8 48.0 + - + +
33O LEU* 4.1 19.5 - - + -
79O VAL* 4.4 18.8 - - + +
98O LEU* 4.1 21.3 - - + -
99O GLU* 3.9 44.4 - - + +
102O ILE* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O LYS* 4.6 11.2 - - + -
7O LEU* 3.1 25.0 + - + +
8O SER* 3.4 11.0 - - - +
10O LEU* 1.3 80.3 - - - +
12O ALA* 1.3 62.6 + - - +
14O LEU* 3.4 10.1 + - - +
15O LYS* 3.2 31.9 + - - +
30O ALA* 4.1 6.5 - - + +
33O LEU* 3.8 48.9 - - + +
34O GLU* 4.0 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12770 C 3.3 46.7 - - - +
8O SER 3.1 13.1 + - - +
9O SER* 3.7 9.4 - - - +
11O ILE* 1.3 78.4 - - - +
13O ASP* 1.3 61.5 + - - +
15O LYS* 3.3 6.0 + - - +
16O SER* 3.1 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 13 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O SER* 2.9 30.0 + - - +
10O LEU* 3.5 8.0 - - + +
12O ALA* 1.3 76.4 - - - +
14O LEU* 1.3 64.6 + - - +
16O SER* 3.4 8.3 + - - -
17O ALA* 3.2 24.1 + - - +
99O GLU* 5.4 6.7 - - + +
102O ILE* 3.9 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O LEU* 2.8 32.2 + - + +
11O ILE* 3.6 6.7 - - - +
13O ASP* 1.3 77.4 - - - +
15O LYS* 1.3 61.3 + - - +
17O ALA* 3.6 0.6 + - - +
18O ALA* 3.2 18.0 + - - +
26O TRP* 3.3 52.3 - - + +
29O VAL* 3.9 15.9 - - + -
30O ALA* 3.9 10.1 - - + -
33O LEU* 3.7 29.8 - - + -
98O LEU* 4.4 6.3 - - + -
102O ILE* 3.2 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12770 C 3.5 17.5 + - - +
12780 A 2.6 35.9 + - - +
12790 U 5.4 1.8 + - - -
11O ILE* 3.2 22.3 + - - +
12O ALA* 3.5 7.4 - - - +
13O ASP 3.1 0.4 - - - -
14O LEU* 1.3 73.6 - - - +
16O SER* 1.3 65.0 + - - +
17O ALA 3.0 1.8 - - - -
18O ALA* 3.0 16.3 + - - +
19O ARG* 3.0 40.0 + - - +
27O GLY* 5.3 2.9 - - - -
30O ALA* 4.1 14.6 - - + -
31O GLU* 6.4 1.6 - - - -
34O GLU* 2.9 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12770 C 3.5 31.4 + - - -
12O ALA 3.1 12.8 + - - -
13O ASP* 3.8 9.0 - - - -
15O LYS* 1.3 79.2 - - - +
17O ALA* 1.3 57.4 + - - +
19O ARG* 4.0 2.0 - - - +
20O SER* 3.0 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O ASP 3.2 10.5 + - - +
14O LEU 3.8 4.7 - - - +
15O LYS 3.0 0.8 - - - -
16O SER* 1.3 75.0 - - - +
18O ALA* 1.3 59.7 + - - +
19O ARG 3.2 2.2 - - - -
20O SER* 4.9 0.9 - - - -
21O SER* 3.1 36.0 + - - +
26O TRP* 3.9 13.7 - - + -
102O ILE* 3.5 32.3 - - + -
106O PRO* 3.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O LEU 3.2 10.3 + - - +
15O LYS* 3.0 6.3 + - - +
17O ALA* 1.3 78.9 - - - +
19O ARG* 1.3 60.1 + - + +
21O SER 3.2 9.1 - - - +
22O GLY 4.5 0.3 - - - -
23O GLY 3.1 31.6 - - - +
24O ALA* 5.0 0.7 - - - -
26O TRP* 3.9 4.2 - - + +
27O GLY* 3.3 36.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12760 U 3.3 57.8 + - - +
12770 C 2.6 41.5 + - - -
12780 A 2.7 42.0 + - - -
15O LYS* 3.0 34.0 + - - +
16O SER* 4.0 2.9 - - - +
18O ALA* 1.3 81.1 - - + +
20O SER* 1.3 70.1 + - - +
21O SER 3.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12760 U 5.1 4.7 + - - -
16O SER* 3.0 22.6 + - - -
17O ALA* 4.9 0.9 - - - -
19O ARG* 1.3 78.9 - - - +
21O SER* 1.3 71.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17O ALA* 3.1 9.1 + - - -
18O ALA 3.2 19.6 - - - +
19O ARG 3.3 2.6 - - - +
20O SER* 1.3 85.0 - - - +
22O GLY* 1.3 59.8 + - - +
23O GLY 3.1 2.9 - - - -
106O PRO* 3.0 51.7 - - - +
107O GLU* 3.6 14.2 + - - -
----------------------------------------------------------
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