Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 3ONC
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 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 2.9 33.7 + - - +
21A LYS 4.9 1.0 - - - +
22A SER* 3.1 27.6 + - - +
24A PRO* 4.7 9.2 - - + -
27A VAL* 4.3 11.0 - - + +
44A CYS* 6.0 0.3 - - - +
45A ALA 4.6 1.6 + - - +
48A TYR* 3.5 23.9 + - - +
49A GLN* 1.3 78.9 - - - +
51A GLU* 1.3 68.8 + - - +
52A ASN 3.3 2.7 - - - -
53A GLU* 3.2 15.4 + - - +
54A VAL* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A CYS* 3.3 14.9 - - + +
45A ALA 3.3 35.8 + - - +
46A HIS* 3.5 12.5 + - - +
49A GLN* 4.7 0.4 - - - +
50A ASN* 1.3 80.2 - - - +
52A ASN* 1.3 64.1 + - - +
54A VAL* 4.2 3.1 - - - -
55A GLY 2.9 18.2 + - - -
76A SER* 2.6 27.1 + - - -
95A THR* 2.7 34.3 + - - +
98A ASP* 3.3 22.9 - - + +
99A LEU* 3.5 14.7 - - + +
800A CIT 3.2 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 1.3 75.8 - - - +
53A GLU* 1.3 68.0 + - - +
55A GLY 3.2 0.9 + - - -
56A VAL* 3.0 31.0 + - - +
98A ASP* 3.5 17.6 - - + +
100A LYS* 2.8 35.3 + - - -
800A CIT 3.0 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 3.4 34.2 - - + +
27A VAL* 3.5 19.5 - - + -
28A THR* 2.8 31.4 + - - +
50A ASN* 3.2 9.5 + - - +
52A ASN* 1.3 79.4 + - + +
54A VAL* 1.3 67.1 + - - +
56A VAL* 3.3 13.9 + - + +
57A ALA 3.5 4.2 + - - -
800A CIT 2.6 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 4.1 15.0 - - + +
27A VAL* 3.8 25.1 - - + -
31A VAL* 4.3 11.9 - - + -
42A ILE* 4.2 11.4 - - + -
44A CYS* 3.9 15.0 - - + -
50A ASN* 3.0 27.1 + - - +
51A GLU* 3.7 7.4 - - - +
53A GLU* 1.3 75.3 - - - +
55A GLY* 1.3 63.2 + - - +
57A ALA* 3.1 6.9 + - - +
58A ILE* 3.1 32.6 + - + +
99A LEU* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU 2.9 15.2 + - - -
52A ASN 3.5 4.5 - - - -
54A VAL* 1.3 74.2 - - - +
56A VAL* 1.3 65.8 + - - +
58A ILE* 3.8 3.3 - - - +
59A GLN* 2.9 27.5 + - - +
98A ASP 3.7 1.6 - - - -
99A LEU* 3.4 29.5 - - - +
100A LYS* 3.3 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.9 19.1 - - + +
32A LYS* 5.3 4.3 - - - +
52A ASN* 3.0 28.4 + - - +
53A GLU* 3.6 12.1 - - + +
54A VAL 3.3 0.4 - - - -
55A GLY* 1.3 75.4 - - - +
57A ALA* 1.3 62.4 + - - +
59A GLN* 3.6 3.1 + - - +
60A GLU* 3.0 24.8 + - + +
100A LYS* 4.0 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.3 35.2 - - + +
31A VAL* 3.5 22.2 - - + -
32A LYS* 3.8 15.3 - - + +
53A GLU 3.5 1.8 + - - -
54A VAL 3.1 10.1 + - - +
56A VAL* 1.3 77.9 - - - +
58A ILE* 1.3 65.4 + - - +
60A GLU* 3.3 1.9 + - - +
61A LYS* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.2 13.5 - - + -
35A ILE* 4.5 11.7 - - + -
42A ILE* 4.8 2.2 - - + -
54A VAL* 3.1 31.7 + - + +
55A GLY* 3.3 6.7 + - - +
57A ALA* 1.3 74.4 - - - +
59A GLN* 1.3 63.5 + - - +
61A LYS* 3.2 3.8 + - - +
62A LEU* 2.9 40.5 + - + +
72A LEU* 3.9 17.8 - - + +
74A ILE* 3.8 36.1 - - + -
99A LEU* 4.4 12.8 - - + +
101A LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 2.9 17.7 + - - +
56A VAL* 3.9 4.7 - - - +
58A ILE* 1.3 79.3 - - - +
60A GLU* 1.3 57.9 + - - +
62A LEU* 3.3 14.9 + - - +
63A ARG* 2.8 42.8 + - + +
100A LYS* 4.0 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 4.2 25.4 - - - +
56A VAL* 3.0 20.5 + - + +
57A ALA 3.8 3.1 - - - +
59A GLN* 1.3 76.6 - - - +
61A LYS* 1.3 58.8 + - + +
63A ARG* 2.8 47.8 + - - -
64A GLU* 2.8 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 3.6 37.1 - - + +
35A ILE* 4.0 34.1 - - + -
36A ASP* 2.8 36.8 + - - +
57A ALA 3.0 20.1 + - - +
58A ILE 3.9 3.6 - - - +
60A GLU* 1.3 78.2 - - - +
62A LEU* 1.3 59.4 + - - +
64A GLU* 2.9 27.0 + - - +
65A GLN 3.2 2.1 + - - -
66A VAL* 3.0 40.5 + - + +
67A VAL* 3.7 8.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 2.9 37.8 + - + +
59A GLN* 3.7 20.0 - - - +
61A LYS* 1.3 73.8 - - - +
63A ARG* 1.3 65.4 + - - +
65A GLN* 3.0 18.4 + - - +
67A VAL* 3.6 15.5 - - + +
68A LYS* 3.7 2.0 - - - -
69A ARG* 3.4 51.8 - - + +
72A LEU* 4.0 12.6 - - + -
100A LYS 5.5 0.4 - - - +
101A LEU* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 2.8 34.8 + - + +
60A GLU* 2.8 43.3 + - - +
62A LEU* 1.3 74.3 - - - +
64A GLU* 1.3 69.7 + - - +
65A GLN* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 2.8 43.1 + - - +
61A LYS* 2.9 39.3 + - - +
63A ARG* 1.3 83.8 + - - +
65A GLN* 1.3 67.7 + - - +
66A VAL* 3.3 16.8 + - + +
----------------------------------------------------------
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