Contacts of the helix formed by residues 27 - 42 (chain E) in PDB entry 1EA4
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 SER 27 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY* 2.9 29.4 + - - -
26B LEU 5.5 0.2 - - - -
21E ALA* 4.2 0.9 - - - -
26E LEU* 1.3 75.5 - - - +
28E LYS* 1.3 66.1 + - - +
29E SER* 3.3 3.8 + - - -
30E ALA* 2.8 24.1 + - - +
31E MET* 2.9 21.5 + - - +
203X A 3.5 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 3.8 31.9 - - + -
7D ILE* 5.2 2.0 - - + -
14E LEU* 4.0 13.7 - - + -
17E LEU* 4.0 31.4 - - + -
18E GLU* 3.3 34.9 + - - +
21E ALA* 4.4 4.0 - - + +
26E LEU 4.0 0.2 + - - -
27E SER* 1.3 74.6 - - - +
29E SER* 1.3 64.6 + - - +
31E MET* 3.4 2.2 + - - +
32E ILE* 3.0 31.3 + - + +
203X A 4.8 3.0 + - - +
204X T 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D THR 4.7 0.5 + - - -
7D ILE* 3.5 18.9 - - - +
8D THR* 3.4 30.8 + - - -
9D LEU* 3.8 5.7 - - - +
27E SER* 3.1 1.5 + - - -
28E LYS* 1.3 79.4 - - - +
30E ALA* 1.3 64.2 + - - +
32E ILE* 3.3 5.2 + - - +
33E SER* 2.9 22.2 + - - -
202X G 5.1 0.2 - - - -
203X A 2.7 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET 5.0 2.9 - - - +
25B GLY* 3.6 19.1 - - - +
26E LEU* 3.8 15.9 - - + -
27E SER* 2.8 24.2 + - - +
29E SER* 1.3 73.7 - - - +
31E MET* 1.3 69.5 + - - +
33E SER* 2.7 20.1 + - - -
34E VAL* 2.8 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 4.7 2.2 - - + -
39D TYR* 3.3 33.7 - - + -
17E LEU* 3.4 25.1 - - + -
20E MET* 3.9 26.5 - - + -
21E ALA* 4.2 11.2 - - + +
24E MET* 3.4 28.3 - - - +
26E LEU* 3.8 8.4 - - + +
27E SER 2.9 13.7 + - - +
28E LYS 3.5 4.0 - - - +
30E ALA* 1.3 79.8 - - - +
32E ILE* 1.3 60.0 + - - +
34E VAL* 3.0 17.2 + - + -
35E ALA* 2.8 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 5.3 0.7 - - + -
7D ILE* 3.8 37.5 - - + -
9D LEU* 5.0 1.3 - - + -
32D ILE* 3.9 30.3 - - + -
36D LEU* 4.6 5.2 - - + -
7E ILE* 4.3 11.4 - - + -
9E LEU* 5.2 0.4 - - + -
17E LEU* 4.0 27.4 - - + -
28E LYS* 3.0 17.2 + - + +
29E SER* 3.4 6.5 - - - +
31E MET* 1.3 72.4 - - - +
33E SER* 1.3 60.3 + - - +
35E ALA* 3.2 7.0 + - - +
36E LEU* 2.7 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 4.1 14.1 - - - -
13D VAL* 4.1 18.5 - - - +
29E SER 2.9 11.5 + - - -
30E ALA* 2.7 18.2 + - - -
32E ILE* 1.3 73.5 - - - +
34E VAL* 1.3 54.8 + - - +
36E LEU* 3.2 10.8 + - - +
37E GLU* 2.8 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TYR* 4.0 21.8 - - + +
24E MET* 5.2 4.7 - - + -
26E LEU* 3.9 16.6 - - + -
30E ALA* 2.8 26.9 + - + +
31E MET* 3.2 15.3 - - + +
33E SER* 1.3 78.6 - - - +
35E ALA* 1.3 53.7 + - - +
37E GLU* 3.2 5.9 + - + +
38E ASN* 2.7 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ALA* 4.3 2.4 - - + +
36D LEU* 3.8 33.2 - - + +
39D TYR* 3.8 33.3 - - + +
31E MET* 2.8 15.9 + - + +
32E ILE* 3.5 7.6 - - + +
34E VAL* 1.3 73.1 - - - +
36E LEU* 1.3 52.6 + - - +
38E ASN* 3.2 0.9 + - - +
39E TYR* 2.6 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 4.1 11.4 - - + -
13D VAL* 4.0 26.2 - - + -
17D LEU* 3.8 32.5 - - + -
20D MET* 4.1 19.2 - - + +
31D MET* 4.8 4.7 - - + -
32D ILE* 4.8 7.0 - - + -
35D ALA* 4.3 17.0 - - + +
32E ILE* 2.7 43.9 + - + +
33E SER* 3.3 4.3 - - - +
35E ALA* 1.3 72.8 - - - +
37E GLU* 1.3 65.7 + - - +
39E TYR* 2.9 7.8 + - + +
40E LYS* 2.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D VAL* 3.1 34.1 - - + +
16D ASN* 4.7 3.1 - - - +
33E SER* 2.8 30.7 + - - +
34E VAL* 3.5 6.7 - - + +
36E LEU* 1.3 72.6 - - - +
38E ASN* 1.3 62.7 + - - +
40E LYS* 2.8 42.1 - - - +
41E LYS* 2.8 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASN* 4.8 3.1 - - - +
39D TYR* 3.4 40.0 - - + -
43D GLN 4.5 5.2 + - - +
34E VAL* 2.7 22.1 + - + +
35E ALA 3.6 2.7 - - - +
37E GLU* 1.3 73.0 - - - +
39E TYR* 1.3 68.6 + - - +
41E LYS* 3.4 7.9 - - - +
42E GLY* 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D MET* 3.8 24.0 - - + -
24D MET* 3.3 30.9 - - - +
31D MET* 4.0 13.0 - - - -
34D VAL* 3.9 20.1 - - + +
35D ALA* 3.9 23.8 - - + +
38D ASN* 3.6 39.5 - - + -
39D TYR 6.1 0.4 - - - +
35E ALA 2.6 21.8 + - - +
36E LEU* 3.3 4.5 - - + +
38E ASN* 1.3 78.4 + - - +
40E LYS* 1.3 67.0 + - - +
42E GLY* 3.2 18.9 + - - +
43E GLN* 3.3 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASN* 2.7 32.8 - - - +
20D MET* 3.6 21.5 - - + -
36E LEU 2.9 11.0 + - - +
37E GLU* 2.8 35.2 - - - +
39E TYR* 1.3 76.8 - - - +
41E LYS* 1.3 84.5 + - - +
43E GLN* 2.5 30.5 + - + +
44E GLU* 2.7 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E GLU 2.8 15.6 + - - +
38E ASN* 3.4 10.8 - - - +
40E LYS* 1.3 88.4 - - - +
42E GLY* 1.3 57.1 + - - +
43E GLN 2.8 5.7 + - - -
44E GLU* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ASN 3.1 9.6 + - - -
39E TYR 3.2 7.6 - - - +
40E LYS 2.8 4.2 + - - -
41E LYS* 1.3 76.5 - - - +
43E GLN* 1.3 71.8 + - - +
44E GLU 5.3 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