Contacts of the helix formed by residues 25 - 39 (chain A) in PDB entry 2DMT
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 25 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 5.5 1.6 - - + +
24A PHE* 1.3 74.3 - - - +
26A GLU* 1.3 68.3 + - - +
27A LEU* 3.9 8.3 + - - +
28A GLN* 2.7 56.3 + - - +
29A LEU* 2.9 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE 3.8 1.8 + - - -
25A THR* 1.3 70.2 - - - +
27A LEU* 1.3 56.7 + - - +
29A LEU* 3.9 16.9 - - - +
30A MET* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 2.7 12.2 + - - +
26A GLU* 1.3 73.4 - - - +
28A GLN* 1.3 70.5 + - + +
30A MET* 3.2 30.8 + - + +
31A GLY* 3.2 9.2 + - - -
54A LEU* 4.2 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL 4.1 3.8 - - - +
24A PHE* 3.4 11.5 - - + -
25A THR* 2.7 49.7 + - - +
27A LEU* 1.3 77.4 - - + +
29A LEU* 1.3 62.6 + - - +
31A GLY* 3.1 4.3 + - - -
32A LEU* 2.9 25.3 + - - +
54A LEU* 3.9 28.0 + - + +
55A GLY 4.8 5.1 + - - -
56A LEU* 3.4 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.5 38.3 - - + +
25A THR 2.9 13.9 + - - +
26A GLU* 3.9 17.9 - - - +
28A GLN* 1.3 72.9 - - - +
30A MET* 1.3 64.9 + - - +
32A LEU* 3.0 4.6 + - + +
33A GLU* 2.8 38.9 + - + +
64A TRP* 3.7 37.0 - - + +
68A ARG* 4.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU 3.0 15.9 + - - +
27A LEU* 3.3 27.4 - - + +
29A LEU* 1.3 76.0 - - - +
31A GLY* 1.3 63.0 + - - +
33A GLU* 3.6 10.4 + - - +
34A LYS* 3.2 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 3.2 3.6 + - - -
28A GLN 3.1 6.6 + - - -
30A MET* 1.3 78.3 - - - +
32A LEU* 1.3 65.7 - - - +
34A LYS* 3.1 8.1 + - - +
35A ARG* 3.0 28.3 + - - +
50A LEU* 5.5 0.2 - - - -
54A LEU* 4.0 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.6 29.8 - - + -
28A GLN 2.9 16.8 + - - +
29A LEU* 3.0 8.7 + - - +
31A GLY* 1.3 75.6 - - - +
33A GLU* 1.3 61.5 + - - +
35A ARG* 4.0 3.4 - - - +
36A PHE* 3.1 21.0 + - - +
50A LEU* 4.3 9.4 - - + -
54A LEU* 3.9 2.6 - - + +
56A LEU* 3.5 32.1 - - + -
60A GLN 5.3 0.2 - - - -
61A VAL* 4.1 28.3 - - + +
64A TRP* 3.2 48.9 - - + -
65A TYR* 4.3 2.9 + - + -
----------------------------------------------------------
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 LEU* 2.8 32.6 + - + +
30A MET* 3.9 7.9 + - - +
32A LEU* 1.3 73.8 - - - +
34A LYS* 1.3 64.4 + - - +
36A PHE* 4.7 1.1 - - - -
37A GLU* 2.9 37.4 + - + +
64A TRP* 3.7 22.4 - - + -
68A ARG* 4.4 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 3.2 29.4 + - - +
31A GLY* 3.1 12.7 + - - +
33A GLU* 1.3 80.3 - - - +
35A ARG* 1.3 66.4 + - + +
37A GLU* 3.7 3.2 - - - +
38A LYS* 3.1 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 3.0 14.3 + - - +
32A LEU 4.0 1.8 - - - +
34A LYS* 1.3 74.6 - - + +
36A PHE* 1.3 69.1 + - - +
38A LYS* 2.8 17.2 + - - +
39A GLN* 2.8 22.5 + - - +
42A LEU* 4.3 16.2 - - + +
46A ASP 5.6 1.2 + - - -
49A ASP* 4.9 8.9 + - - +
50A LEU* 3.8 56.4 - - + +
53A SER* 4.7 10.7 + - - -
65A TYR* 3.5 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 3.1 17.4 + - - +
33A GLU* 4.2 2.2 - - - +
35A ARG* 1.3 72.4 - - - +
37A GLU* 1.3 76.4 + - + +
39A GLN 2.8 23.8 - - - -
40A LYS* 3.0 32.4 + - + +
64A TRP* 3.8 9.2 - + + -
65A TYR* 2.9 79.9 + + + -
68A ARG* 3.6 21.1 - - + -
69A ARG* 3.9 22.4 - - + -
72A TRP* 5.0 10.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.9 29.4 + - + +
34A LYS* 3.7 5.6 - - - +
36A PHE* 1.3 88.3 - - + +
38A LYS* 1.3 65.0 + - + +
40A LYS* 3.4 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.1 37.0 + - + +
35A ARG* 2.8 18.5 + - - +
37A GLU* 1.3 79.6 - - + +
39A GLN* 1.3 62.9 + - + +
40A LYS* 4.2 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG 2.8 10.0 + - - +
36A PHE* 2.8 15.6 - - - +
38A LYS* 1.3 75.1 - - + +
40A LYS* 1.3 68.7 + - - +
41A TYR* 2.8 29.6 + - - +
42A LEU* 3.7 28.0 + - + +
43A SER* 4.3 8.5 + - - +
46A ASP* 4.1 14.6 + - - -
65A TYR* 3.6 6.9 + - - -
----------------------------------------------------------
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