Contacts of the helix formed by residues 21 - 34 (chain A) in PDB entry 2DT4
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 GLU 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 3.8 1.2 + - - -
20A GLU* 1.3 75.8 + - - +
22A LEU* 1.3 67.5 + - - +
23A LEU* 3.1 22.1 + - - +
24A THR* 2.7 46.7 + - - +
25A TYR* 2.9 21.8 + - - +
108A GLU* 3.3 22.2 - - + +
109A GLY 2.9 37.2 + - - +
110A GLU* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.0 22.2 - - + -
20A GLU 3.6 2.2 + - - -
21A GLU* 1.3 72.7 + - - +
23A LEU* 1.3 63.2 + - + +
25A TYR* 3.3 3.0 + - - +
26A ILE* 3.0 42.2 + - + +
46A LEU* 4.2 18.8 - - + -
72A LEU* 4.3 10.8 - - + -
75A LEU* 3.5 30.3 - - + -
106A LEU* 4.3 12.3 - - + -
109A GLY 2.9 18.6 + - - +
111A VAL* 3.8 20.9 - - + -
114A ALA* 4.0 6.7 - - + -
116A ILE* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.1 14.7 + - - +
22A LEU* 1.3 75.7 - - + +
24A THR* 1.3 62.7 + - - +
26A ILE* 3.3 6.9 + - + -
27A LYS* 3.0 24.7 + - - +
75A LEU* 5.6 0.7 - - + -
88A VAL* 3.7 42.0 - - + +
90A ALA* 4.4 14.1 - - + +
105A HIS* 5.6 0.7 - - - +
106A LEU* 3.4 48.0 - - + +
107A VAL 3.4 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 5.2 4.5 - - - +
21A GLU* 2.7 37.5 + - + +
23A LEU* 1.3 76.1 - - - +
25A TYR* 1.3 63.0 + - - +
27A LYS* 3.3 9.0 + - + +
28A ASN* 2.9 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.6 36.4 - + - +
15A ARG 4.5 2.9 + - - -
16A VAL* 3.7 25.8 - - + -
17A PRO* 3.6 25.3 - - + +
20A GLU* 3.6 36.9 + - + +
21A GLU 2.9 16.4 + - - +
22A LEU 3.7 3.8 - - - +
24A THR* 1.3 75.6 - - - +
26A ILE* 1.3 63.8 + - + +
28A ASN* 3.2 7.0 + - + +
29A PHE* 2.8 45.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 5.3 3.6 - - + -
22A LEU* 3.0 46.2 + - + +
23A LEU* 3.9 5.8 - - + +
25A TYR* 1.3 84.6 - - + +
27A LYS* 1.3 62.5 + - - +
29A PHE* 3.4 5.1 + - + +
30A CYS* 3.0 22.7 + - - -
40A ILE* 4.2 21.3 - - + -
75A LEU* 5.2 3.8 - - + -
79A VAL* 4.2 15.0 - - + -
88A VAL* 3.9 23.8 - - + -
116A ILE* 4.6 22.4 - - + -
118A LEU* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.0 14.2 + - - +
24A THR* 3.5 11.9 - - + +
26A ILE* 1.3 76.6 - - - +
28A ASN* 1.3 61.4 + - - +
30A CYS* 3.2 7.2 + - - +
31A LYS* 2.9 65.5 + - + +
85A GLU* 4.4 10.7 - - - +
86A PRO* 3.6 24.2 + - - +
87A PHE* 5.5 7.5 - - + -
88A VAL* 3.6 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 5.4 2.8 + - - -
24A THR* 2.9 38.8 + - - +
25A TYR* 3.7 7.0 - - + +
27A LYS* 1.3 78.6 - - - +
29A PHE* 1.3 66.5 + - - +
31A LYS* 3.3 20.4 + - - +
32A LYS* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.4 40.2 - + - -
14A PHE* 3.9 26.0 - + - -
25A TYR* 2.8 42.5 + - + +
26A ILE* 3.5 5.2 - - - +
28A ASN* 1.3 73.1 - - - +
30A CYS* 1.3 61.7 + - - +
32A LYS* 3.2 6.7 + - + +
33A GLU* 2.9 46.6 + - + +
35A ILE* 3.6 21.1 - - + -
118A LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE 3.0 18.9 + - - +
27A LYS* 3.7 7.2 - - - +
29A PHE* 1.3 79.0 - - - +
31A LYS* 1.3 63.8 + - - +
33A GLU 3.3 0.2 + - - -
34A GLY* 2.9 19.9 + - - -
35A ILE* 2.9 52.4 + - + +
79A VAL* 3.9 26.5 - - - -
86A PRO* 4.0 10.5 - - + -
118A LEU* 4.0 17.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
27A LYS* 2.9 57.4 + - - +
28A ASN* 3.7 21.3 + - - +
29A PHE 3.2 0.4 - - - -
30A CYS* 1.3 77.8 - - - +
32A LYS* 1.3 62.6 + - - +
34A GLY* 3.3 9.5 + - - -
85A GLU* 3.4 25.2 + - - +
86A PRO* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN 3.0 17.9 + - - +
29A PHE* 3.5 6.7 - - + +
31A LYS* 1.3 78.1 - - - +
33A GLU* 1.3 75.2 + - - +
34A GLY 3.4 0.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
10A ARG* 2.8 36.8 + - - +
12A TYR* 2.7 34.6 + - - +
29A PHE* 2.9 42.2 + - + +
32A LYS* 1.3 90.9 + - + +
34A GLY* 1.3 56.8 + - - +
35A ILE* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 3.5 9.8 + - - -
30A CYS 2.9 6.1 + - - -
31A LYS* 3.3 7.4 + - - -
32A LYS 3.2 4.4 + - - -
33A GLU* 1.3 78.5 - - - +
35A ILE* 1.3 61.3 + - - +
36A GLU* 3.9 7.7 + - - +
120A GLU* 4.1 2.8 - - - +
122A LYS* 5.1 1.9 + - - -
----------------------------------------------------------
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