Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 1OQY
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 24 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP 3.9 1.6 + - - -
23A GLU* 1.3 78.9 + - - +
25A VAL* 1.3 61.7 + - - +
26A LYS* 2.7 21.1 + - + +
27A VAL* 2.9 23.0 + - - +
28A LEU 3.9 0.3 + - - -
57A ASP 4.0 15.5 - - - +
58A ASP* 4.4 5.2 - - - -
59A VAL 4.4 11.2 - - - +
60A PRO* 3.5 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 3.2 1.5 + - - -
24A THR* 1.3 72.2 - - - +
26A LYS* 1.3 55.5 + - - +
27A VAL 3.1 0.4 - - - -
28A LEU* 2.6 38.8 + - + +
29A LYS 3.2 3.3 + - - +
48A LEU* 3.3 30.5 - - + -
55A LEU* 4.9 3.1 - - + -
56A SER 2.7 29.8 - - - +
57A ASP* 3.5 9.1 - - + +
59A VAL 2.6 32.5 + - - +
60A PRO 4.2 1.1 - - - -
61A ILE* 4.0 23.3 - - + +
64A TYR* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 2.7 14.8 + - + +
25A VAL* 1.3 78.7 - - - +
27A VAL* 1.3 65.6 + - + +
28A LEU 3.1 0.5 + - - -
29A LYS* 3.2 23.7 + - + +
30A GLU* 2.9 38.2 + - - +
43A VAL* 5.4 4.8 - - - +
57A ASP* 3.4 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 5.5 3.4 - - + -
23A GLU* 3.4 44.0 - - + +
24A THR* 2.9 13.8 + - - +
26A LYS* 1.3 78.0 - - + +
28A LEU* 1.3 50.5 + - - +
30A GLU* 3.2 12.3 + - + +
31A LYS* 2.6 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.4 3.8 - - + -
7A LEU* 4.2 8.7 - - + -
17A ILE* 4.5 5.4 - - + -
19A MET* 3.2 33.4 - - + -
24A THR 3.9 0.6 + - - -
25A VAL* 2.6 37.1 + - + +
27A VAL* 1.3 73.5 - - - +
29A LYS* 1.3 54.7 + - - +
31A LYS* 2.6 26.4 + - + +
32A ILE* 2.7 40.2 + - + +
48A LEU* 3.5 24.5 - - + -
61A ILE* 4.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL 3.2 1.7 + - - +
26A LYS* 3.4 18.2 - - - +
28A LEU* 1.3 80.6 - - - +
30A GLU* 1.3 63.3 + - + +
32A ILE* 4.0 1.1 - - - -
33A GLU* 3.3 18.9 + - - +
43A VAL* 3.7 28.2 + - + +
46A GLN* 2.9 67.9 + - + +
48A LEU* 5.2 5.4 - - + -
57A ASP* 2.9 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 2.9 49.6 + - - +
27A VAL* 3.2 11.9 + - + +
28A LEU 3.0 0.6 - - - -
29A LYS* 1.3 78.8 - - + +
31A LYS* 1.3 65.3 + - - +
33A GLU* 3.3 18.6 + - - +
34A ALA* 3.3 20.8 + - - +
43A VAL* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.3 30.5 - - + -
19A MET* 3.8 39.3 - - + +
27A VAL* 2.6 33.8 + - + +
28A LEU* 2.6 19.5 + - + +
30A GLU* 1.3 73.1 - - - +
32A ILE* 1.3 49.8 + - - +
34A ALA* 3.3 7.2 + - + +
35A GLU* 2.6 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.7 12.6 - - + -
15A PHE* 5.3 1.1 - - + -
17A ILE* 5.0 0.9 - - + -
28A LEU* 2.7 44.9 + - + +
29A LYS* 4.0 1.6 - - - +
31A LYS* 1.3 71.8 - - - +
33A GLU* 1.3 65.7 + - - +
35A GLU* 3.8 7.0 - - - -
36A LYS* 2.9 24.7 + - + +
37A GLY 3.5 2.8 + - - +
41A PHE* 3.5 29.6 - - + -
46A GLN* 3.3 36.3 - - + +
48A LEU* 4.0 3.4 - - + -
74A VAL* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS 3.3 11.6 + - - +
30A GLU* 3.3 21.8 + - - +
32A ILE* 1.3 78.6 - - - +
34A ALA* 1.3 57.8 + - - +
37A GLY* 2.5 35.3 - - - +
38A ARG* 3.3 34.1 - - + +
41A PHE 3.7 20.4 - - - +
42A PRO* 4.5 3.1 - - - +
43A VAL* 3.7 25.8 - - + +
46A GLN* 4.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU 3.3 12.2 + - - +
31A LYS* 3.9 7.2 - - + +
32A ILE 3.1 0.2 - - - -
33A GLU* 1.3 79.8 - - + +
35A GLU* 1.3 67.2 + - - +
36A LYS 4.6 0.2 - - - -
37A GLY* 4.0 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.1 44.6 - - + +
16A LYS 3.8 16.5 - - - +
17A ILE* 4.0 24.6 - - + +
31A LYS* 2.6 26.6 + - - +
32A ILE* 3.8 8.5 - - - +
34A ALA* 1.3 77.7 - - - +
36A LYS* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 6.2 0.4 - - - -
13A GLN* 3.8 24.6 - - - +
15A PHE* 3.0 44.1 - - + -
32A ILE 2.9 6.8 + - - +
34A ALA 4.6 0.2 - - - -
35A GLU* 1.3 78.5 - - - +
37A GLY* 1.3 58.5 + - - +
39A ASP* 6.1 0.5 - - - +
41A PHE* 3.5 60.3 - - + -
----------------------------------------------------------
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