Contacts of the helix formed by residues 16 - 29 (chain C) in PDB entry 3IO6
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 GLY 16 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 5.2 2.0 - - - -
15C LYS* 1.3 70.6 - - - +
17C TYR* 1.3 62.9 + - - -
18C ASN 3.4 2.2 - - - -
19C GLY 3.3 2.3 + - - -
20C LEU* 3.2 17.5 + - - +
293C VAL* 3.4 22.7 - - - +
296C ASP* 3.2 20.2 - - - -
297C LYS* 3.6 25.1 + - - +
299C LEU* 5.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.7 24.5 - - + -
12C ASN 4.3 4.5 - - - -
13C GLY 3.3 20.4 - - - -
15C LYS 2.9 26.1 + - - -
16C GLY* 1.3 70.8 - - - -
18C ASN* 1.3 101.2 + - - +
20C LEU* 3.1 8.8 + - - +
21C ALA* 2.8 30.4 + - - +
37C VAL* 3.9 13.2 - - + +
39C HIS* 3.5 50.1 + + + -
296C ASP* 3.6 0.6 + - - -
297C LYS* 5.3 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 1.3 108.7 + - - +
19C GLY* 1.3 58.3 + - - +
21C ALA* 3.6 7.2 + - - +
22C GLU* 2.9 34.1 + - + +
296C ASP* 3.3 22.3 + - - +
297C LYS* 4.3 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLY 3.3 8.1 + - - -
17C TYR 3.2 0.4 - - - -
18C ASN* 1.3 77.4 - - - +
20C LEU* 1.3 58.0 + - - +
22C GLU* 3.6 10.7 - - - +
23C VAL* 3.0 21.5 - - - +
292C ALA* 3.3 31.3 - - - +
293C VAL* 3.6 9.2 - - - +
296C ASP* 3.5 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 3.8 25.1 - - + -
11C ILE* 4.2 17.3 - - + -
16C GLY 3.2 11.2 + - - +
17C TYR* 3.1 8.9 + - - +
19C GLY* 1.3 76.0 - - - +
21C ALA* 1.3 60.4 + - - +
22C GLU 3.2 1.1 - - - -
23C VAL* 3.0 10.0 + - - +
24C GLY* 3.0 22.2 + - - -
37C VAL* 3.7 28.1 - - + +
61C PHE* 3.9 24.2 - - + -
279C PHE* 4.6 10.5 - - + -
284C LEU* 3.8 28.5 - - + -
293C VAL* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR 2.8 15.9 + - - +
18C ASN* 4.0 7.9 - - - +
20C LEU* 1.3 76.4 - - - +
22C GLU* 1.3 58.0 + - - +
24C GLY* 3.0 4.3 + - - +
25C LYS* 3.0 28.4 + - - +
35C VAL 6.0 2.0 - - - +
37C VAL* 3.9 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN* 2.9 28.8 + - + +
19C GLY* 3.6 12.3 - - - +
21C ALA* 1.3 76.1 - - - +
23C VAL* 1.3 61.7 + - - +
25C LYS* 3.8 9.3 + - - +
26C LYS* 3.8 13.7 + - - +
292C ALA* 4.7 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLY 3.0 20.9 - - - +
20C LEU* 3.0 11.2 + - - +
22C GLU* 1.3 74.3 - - - +
24C GLY* 1.3 57.4 + - - +
25C LYS 3.0 4.0 - - - -
26C LYS* 2.9 28.1 + - + +
27C PHE* 2.9 40.6 + - + -
279C PHE* 5.1 1.6 - - + -
283C TYR* 4.7 4.3 - - + -
284C LEU* 4.0 17.9 - - + +
289C GLY* 3.7 38.1 - - - +
292C ALA* 3.9 6.7 - - + -
293C VAL* 4.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU 3.0 12.8 + - - -
21C ALA* 3.0 8.0 + - - -
23C VAL* 1.3 75.6 - - - +
25C LYS* 1.3 56.9 + - - +
27C PHE* 3.7 11.6 - - - -
28C GLU* 3.6 16.5 + - - +
35C VAL* 3.3 42.6 - - - +
279C PHE* 4.1 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 3.0 13.2 + - - +
22C GLU* 3.8 11.7 - - - +
23C VAL 3.0 0.4 - - - -
24C GLY* 1.3 75.1 - - - +
26C LYS* 1.3 63.2 + - - +
27C PHE 3.2 2.0 - - - -
28C GLU* 2.9 53.9 + - - +
29C LYS* 3.3 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU 3.8 7.7 + - - +
23C VAL* 2.9 15.1 + - + +
25C LYS* 1.3 74.7 - - - +
27C PHE* 1.3 63.5 + - + +
29C LYS* 3.2 46.7 - - + +
30C ASP* 3.4 30.9 + - - +
283C TYR* 4.6 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 6.3 0.4 - - + -
23C VAL* 2.9 53.4 + - + -
24C GLY* 3.7 8.1 - - - +
25C LYS 3.2 0.4 - - - -
26C LYS* 1.3 77.4 - - - +
28C GLU* 1.3 56.8 + - - +
29C LYS 3.2 1.1 - - - -
30C ASP* 3.0 18.0 + - - +
31C THR* 3.2 20.2 + - - +
32C GLY 3.8 0.9 + - - -
33C ILE* 4.6 3.5 + - + +
35C VAL* 4.5 7.9 - - + -
278C GLU* 5.1 2.2 - - + -
279C PHE* 2.9 78.7 - + + -
283C TYR* 2.9 44.9 - + + -
284C LEU 4.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY 3.6 9.8 + - - +
25C LYS* 2.9 48.8 + - - +
27C PHE* 1.3 77.5 - - - +
29C LYS* 1.3 57.7 + - - +
30C ASP 3.3 0.2 - - - -
32C GLY* 3.0 36.3 - - - +
33C ILE 3.2 16.8 - - - +
34C LYS* 3.2 37.6 - - - +
35C VAL 3.8 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LYS* 3.3 14.3 + - - +
26C LYS* 3.2 50.9 - - + +
27C PHE 3.2 1.2 - - - -
28C GLU* 1.3 77.1 - - - +
30C ASP* 1.3 74.1 + - - +
32C GLY 4.6 0.4 - - - -
----------------------------------------------------------
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