Contacts of the helix formed by residues 9 - 25 (chain O) in PDB entry 5IYB
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 THR 9 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336N VAL* 3.7 30.5 - - + -
357N ILE* 4.5 19.7 - - + +
5O LEU 4.6 1.6 - - - +
6O TYR* 2.6 35.5 + - - +
8O ASN* 1.3 79.8 - - - +
10O THR* 1.3 56.3 - - - +
11O LEU* 3.8 12.1 - - - +
12O GLY 2.8 16.6 + - - -
13O ASN* 2.5 39.0 + - - +
40O PHE* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N LEU* 5.6 4.9 - - - +
359N ASN* 4.8 18.3 + - + +
364N ASP* 4.8 10.4 + - - -
9O THR* 1.3 70.3 - - - +
11O LEU* 1.3 59.0 + - - +
13O ASN* 3.7 6.9 - - - +
14O SER* 2.7 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N TYR* 3.5 41.3 - - + -
17N VAL* 4.9 4.7 - - + -
46N TRP* 3.3 35.5 + - + -
50N LEU* 4.7 8.2 - - + +
357N ILE* 5.2 10.5 - - + -
6O TYR* 6.4 0.7 - - + -
9O THR* 3.8 10.3 + - - +
10O THR* 1.3 80.6 + - - +
12O GLY* 1.3 59.9 + - - +
14O SER* 3.0 17.3 + - - -
15O LEU* 3.4 11.4 + - - +
40O PHE* 3.7 20.7 - - + -
44O ILE* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 12 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O TYR 3.4 13.0 - - - -
7O ARG* 3.7 10.1 - - - -
9O THR* 2.8 23.8 + - - -
11O LEU* 1.3 74.1 - - - +
13O ASN* 1.3 60.2 + - - +
15O LEU* 3.4 6.8 - - - +
16O GLN* 3.3 25.6 + - - +
37O LEU* 4.8 1.1 - - - +
40O PHE* 4.0 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 13 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O ARG 3.7 4.0 + - - +
8O ASN 4.7 3.8 - - - +
9O THR 2.5 21.4 + - - +
10O THR* 3.7 6.8 + - - +
12O GLY* 1.3 70.3 - - - +
14O SER* 1.3 60.6 + - - +
15O LEU 3.2 1.6 - - - -
16O GLN* 3.2 17.4 + - - +
17O GLU* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N TRP* 3.6 15.1 + - - -
49N LYS* 4.0 23.2 - - - +
50N LEU* 4.7 11.9 - - - +
10O THR 2.7 26.6 + - - -
11O LEU* 3.0 17.5 + - - -
13O ASN* 1.3 74.6 - - - +
15O LEU* 1.3 51.1 + - - +
17O GLU* 3.9 6.4 - - - +
18O SER* 2.6 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N VAL* 5.3 7.4 - - + -
42N LEU* 4.7 10.1 - - + -
46N TRP* 3.4 26.4 - - + +
11O LEU 3.4 6.8 + - - +
12O GLY 3.4 8.5 - - - +
13O ASN 3.2 0.4 - - - -
14O SER* 1.3 79.3 + - - +
16O GLN* 1.3 54.8 - - - +
18O SER* 3.1 4.2 + - - -
19O LEU* 2.7 57.7 + - + +
36O VAL* 4.5 12.1 - - + -
37O LEU* 3.7 17.9 - - + -
40O PHE* 3.5 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O ARG* 3.6 44.8 + - - +
12O GLY 3.3 13.1 + - - +
13O ASN* 3.2 17.9 + - - +
15O LEU* 1.3 78.1 - - - +
17O GLU* 1.3 51.1 + - - +
19O LEU* 3.4 9.5 + - - +
20O ASP* 2.7 34.8 + - - +
37O LEU* 3.6 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N LYS* 3.6 26.7 + - + +
13O ASN* 2.9 23.7 + - - +
14O SER* 3.9 6.3 - - - +
16O GLN* 1.3 74.1 - - - +
18O SER* 1.3 61.0 + - - +
20O ASP* 3.2 15.6 + - - +
21O GLU* 2.9 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N LEU* 3.5 23.7 - - - +
45N LEU* 4.8 6.3 - - - +
46N TRP* 3.4 29.6 + - - +
49N LYS* 3.5 11.2 - - - +
14O SER 2.6 23.6 + - - -
15O LEU 3.3 5.4 - - - -
17O GLU* 1.3 75.8 - - - +
19O LEU* 1.3 62.5 + - - +
21O GLU* 3.4 12.0 - - - +
22O LEU* 3.3 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N PHE* 5.7 0.4 - - + -
42N LEU* 4.3 18.4 - - + -
15O LEU* 2.7 35.9 + - + +
16O GLN* 3.5 7.4 - - - +
18O SER* 1.3 72.7 - - - +
20O ASP* 1.3 57.9 - - - +
22O LEU* 3.2 7.5 + - - +
23O ILE* 2.9 33.8 + - + +
28O ILE* 3.8 20.0 - - + +
33O ALA* 3.6 35.9 - - + +
36O VAL* 4.2 22.2 - - + -
37O LEU* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O GLN 2.7 20.7 + - - +
17O GLU* 3.2 19.5 + - - +
19O LEU* 1.3 70.6 - - - +
21O GLU* 1.3 61.7 + - - +
23O ILE* 3.2 11.9 + - - +
24O GLN* 2.9 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N LEU* 4.5 20.0 - - + -
49N LYS* 4.3 21.4 + - - -
17O GLU* 2.9 32.2 + - - +
18O SER* 3.4 12.1 - - - +
20O ASP* 1.3 76.6 - - - +
22O LEU* 1.3 57.5 + - - +
24O GLN* 3.3 7.3 + - - +
25O SER* 2.9 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N PHE* 4.9 0.9 - - + -
38N VAL* 3.5 30.7 - - + +
41N GLU* 5.3 5.4 - - + -
42N LEU* 3.6 48.7 - - + +
45N LEU* 5.2 9.2 - - + -
18O SER 3.3 7.8 + - - +
19O LEU* 3.2 8.9 + - - +
21O GLU* 1.3 78.8 - - + +
23O ILE* 1.3 55.4 + - - +
25O SER* 3.1 4.8 + - - +
26O GLN 2.9 5.2 + - - -
27O GLN* 2.7 40.2 + - + -
28O ILE* 3.6 35.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O LEU* 2.9 23.4 + - + +
20O ASP* 3.2 12.8 + - - +
22O LEU* 1.3 73.2 - - - +
24O GLN* 1.3 74.6 + - - +
26O GLN* 2.8 26.1 + - - +
28O ILE* 4.0 21.1 - - + +
30O PRO* 4.4 27.6 - - + -
33O ALA* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O ASP* 2.9 47.7 + - - +
21O GLU* 3.8 9.2 - - - +
23O ILE* 1.3 86.0 - - - +
25O SER* 1.3 58.6 + - - +
26O GLN* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O GLU 2.9 18.3 + - - -
22O LEU* 3.1 12.1 + - - +
24O GLN* 1.3 74.5 - - - +
26O GLN* 1.3 68.2 + - - +
27O GLN* 3.1 30.1 + - - +
----------------------------------------------------------
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