Contacts of the helix formed by residues 17 - 35 (chain E) in PDB entry 2CHS
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 17 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E THR* 1.3 71.3 - - - +
18E GLU* 1.3 57.1 + - - +
21E LEU* 2.9 47.7 + - + +
55E ALA* 3.6 13.1 - - + +
56E VAL* 3.7 35.3 - - + +
60E LYS* 3.5 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E THR* 3.2 13.2 - - + +
17E GLU* 1.3 79.8 + - - +
19E GLU* 1.3 62.0 + - - +
21E LEU* 4.6 3.9 - - - +
22E GLN* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 3.7 10.1 - - + -
13E GLU* 2.9 21.4 + - - +
14E ARG* 2.9 54.3 + - - +
16E THR* 2.9 19.2 + - + +
18E GLU* 1.3 78.6 - - - +
20E ILE* 1.3 59.2 + - - +
22E GLN* 3.7 15.2 + - - +
23E LYS* 2.8 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 3.8 22.4 - - + -
15E ASP* 3.4 25.8 - - - +
16E THR 2.8 22.2 + - - +
19E GLU* 1.3 73.5 - - - +
21E LEU* 1.4 65.5 + - - +
24E THR* 2.8 29.8 + - - -
53E LEU* 4.4 13.9 - - + -
55E ALA* 3.9 13.2 - - + +
56E VAL* 3.6 29.4 - - + +
58E PRO* 4.1 24.7 - - + -
89E ILE* 3.9 15.1 - - + +
79F MET* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLU* 2.9 44.6 + - + +
18E GLU* 4.6 2.7 - - - +
20E ILE* 1.4 73.0 - - + +
22E GLN* 1.3 56.9 + - - +
24E THR* 4.5 0.4 - - - -
25E LYS* 2.8 32.0 + - - +
56E VAL* 3.9 18.2 - - + -
57E PHE 4.2 3.6 - - - +
58E PRO 4.7 1.6 - - - +
60E LYS* 3.6 43.3 - - + +
61E ALA* 3.5 19.8 - - + +
64E GLU* 5.1 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E GLU* 3.1 20.8 + - + +
19E GLU* 3.7 22.6 + - - +
21E LEU* 1.3 78.7 - - - +
23E LYS* 1.3 74.0 + - - +
25E LYS* 3.3 12.0 + - - +
26E GLN* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E THR* 3.7 14.5 + - + +
11E THR 3.7 23.1 + - - +
12E VAL* 3.9 15.7 - - + -
13E GLU* 4.5 10.9 + - - +
19E GLU* 2.8 54.2 + - - +
22E GLN* 1.3 88.3 - - - +
24E THR* 1.3 64.9 + - - +
26E GLN* 3.6 22.7 + - - +
27E LEU* 3.1 22.3 + - - +
109E LEU* 5.8 0.3 - - - +
110E GLU* 4.0 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E THR* 4.6 2.9 - - - -
20E ILE 2.8 20.1 + - - -
21E LEU 3.8 2.9 - - - -
23E LYS* 1.3 73.8 - - - +
25E LYS* 1.3 64.3 + - - +
27E LEU* 2.9 19.7 + - + +
28E LEU* 2.9 23.5 + - + +
47E LEU* 4.2 17.7 - - + -
58E PRO* 3.5 33.4 - - + +
61E ALA* 3.8 8.1 - - + -
89E ILE* 3.2 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU 2.8 22.2 + - - +
22E GLN* 3.3 11.6 + - - +
24E THR* 1.3 70.4 - - - +
26E GLN* 1.3 62.5 + - - +
28E LEU* 3.2 8.6 + - - +
29E GLU* 2.8 60.3 + - + +
61E ALA* 3.9 17.7 - - + +
64E GLU* 3.1 50.6 + - + +
65E LEU* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 2.9 42.9 + - + +
23E LYS* 3.7 34.9 - - - +
25E LYS* 1.3 82.1 - - + +
27E LEU* 1.3 59.0 + - - +
29E GLU* 3.6 12.7 + - - +
30E LYS* 3.2 22.2 + - - +
109E LEU* 4.4 8.9 - - + +
110E GLU* 4.5 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ALA* 3.6 29.8 - - - +
10E THR* 3.7 24.5 - - + +
23E LYS 3.1 12.5 + - - +
24E THR* 2.9 12.5 + - + +
26E GLN* 1.3 72.0 - - - +
28E LEU* 1.3 67.6 + - + +
30E LYS* 3.2 3.5 + - - +
31E ILE* 3.0 32.8 + - + +
47E LEU* 6.1 1.1 - - + -
89E ILE* 4.2 8.1 - - + +
91E VAL* 3.7 23.1 - - + -
107E VAL* 3.6 36.3 - - + +
109E LEU* 4.2 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E THR* 2.9 30.7 + - + +
25E LYS* 3.7 8.5 - - - +
27E LEU* 1.3 75.5 - - + +
29E GLU* 1.3 57.4 + - - +
31E ILE* 3.3 8.0 + - + +
32E ILE* 2.9 38.8 + - + +
45E MET* 3.6 31.6 - - + -
47E LEU* 4.5 8.7 - - + -
61E ALA 4.6 2.9 - - - -
62E VAL* 3.8 33.2 - - + +
65E LEU* 3.8 26.0 - - + -
91E VAL* 4.5 16.4 - - + -
93E MET* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LYS* 2.8 43.8 + - - +
26E GLN* 3.8 13.8 - - - +
28E LEU* 1.3 75.7 - - - +
30E LYS* 1.3 57.9 + - - +
32E ILE* 3.6 8.5 + - - +
33E GLU* 3.0 30.3 + - - +
64E GLU 5.3 1.9 - - - +
65E LEU* 3.8 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E GLN 3.2 11.8 + - - +
27E LEU 3.2 8.5 + - - +
29E GLU* 1.3 77.0 - - - +
31E ILE* 1.3 64.9 + - - +
33E GLU* 3.1 29.5 + - - +
34E GLU* 2.9 59.9 + - + +
107E VAL* 3.6 24.7 - - + -
109E LEU* 4.4 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 4.0 18.8 - - + +
7E ARG 4.4 6.1 - - - +
8E GLY* 4.0 12.6 - - - +
27E LEU* 3.0 21.9 + - + +
28E LEU* 3.6 11.0 - - + +
30E LYS* 1.3 74.5 - - - +
32E ILE* 1.3 64.2 + - - +
35E ASN* 2.9 31.2 + - - +
91E VAL* 3.5 37.0 - - + -
93E MET* 3.4 34.3 - - + -
107E VAL* 3.7 25.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
28E LEU* 2.9 26.0 + - + +
29E GLU* 3.7 6.5 - - - +
31E ILE* 1.3 73.2 - - - +
33E GLU* 1.3 54.3 + - - +
36E HIS* 2.7 33.1 + - - -
37E THR* 3.2 35.4 + - + +
65E LEU* 3.9 28.7 - - + -
68E TRP* 3.4 40.6 - - + +
93E MET* 5.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLU 3.0 17.6 + - - +
30E LYS* 3.1 40.9 + - - +
32E ILE* 1.3 79.1 - - - +
34E GLU* 1.3 67.0 + - - +
35E ASN 3.3 0.9 + - - -
36E HIS* 3.5 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E LYS* 2.9 62.7 + - + +
33E GLU* 1.3 81.1 - - + +
35E ASN* 1.3 70.2 + - - +
36E HIS* 3.7 11.8 - - - -
105E ARG* 3.5 43.7 + - + +
106E HIS 5.7 0.2 - - - +
107E VAL* 4.1 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 3.8 16.8 - - + +
31E ILE* 2.9 31.1 + - - +
34E GLU* 1.3 82.8 - - - +
36E HIS* 1.4 75.0 + - - +
37E THR* 3.2 16.1 + - - +
104E ILE* 3.8 12.5 - - - +
105E ARG* 2.8 53.1 + - - +
----------------------------------------------------------
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