Contacts of the helix formed by residues 16 - 40 (chain E) in PDB entry 2AXT
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 16 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ASP 2.9 9.7 + - - -
13E ILE* 2.5 30.9 + - - +
15E THR* 1.3 75.6 - - - +
17E VAL* 1.3 67.0 + - - +
18E ARG* 4.2 6.6 - - - +
19E TYR* 2.9 28.5 + - - +
20E TRP* 3.2 8.8 - - - -
51F HEM 5.3 2.3 + - - -
7J ARG* 4.9 1.8 - - - +
8J ILE* 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR 3.4 2.8 + - - -
16E SER* 1.3 72.7 - - - +
18E ARG* 1.3 63.4 + - - +
19E TYR 3.2 0.2 + - - -
20E TRP* 3.2 5.6 + - + +
21E VAL* 2.9 30.1 + - + +
7J ARG* 3.5 21.3 - - + -
8J ILE* 3.4 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E SER* 3.1 7.5 - - - +
17E VAL* 1.3 80.9 - - - +
19E TYR* 1.3 55.8 + - - +
21E VAL* 3.0 11.9 + - + +
22E ILE* 2.7 51.5 + - + +
15F ILE* 4.8 14.8 - - - +
16F PHE* 5.4 5.3 - - - -
51F HEM 3.3 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ILE* 3.1 27.8 - - + +
14E ILE* 4.7 6.1 - - + -
16E SER* 2.9 29.1 + - - +
18E ARG* 1.3 79.5 - - - +
20E TRP* 1.3 103.5 + + - +
22E ILE* 3.2 8.9 + - - +
23E HIS* 2.8 70.6 + + + +
27E ILE* 4.6 5.5 - - + +
51F HEM 3.2 57.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ILE* 2.6 34.6 + - + -
16E SER 3.2 22.4 + - - -
17E VAL* 3.2 4.1 + - + +
19E TYR* 1.3 102.8 - + - +
21E VAL* 1.3 61.3 + - - +
23E HIS* 4.2 4.0 - - + +
24E SER* 2.8 42.4 + - - +
27E ILE* 5.6 8.3 - - + -
8J ILE* 3.5 30.9 - - + +
13J VAL* 3.5 32.8 - - + -
17J ALA* 6.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 2.9 31.3 + - + +
18E ARG* 3.0 12.7 + - + +
20E TRP* 1.3 78.5 - - - +
22E ILE* 1.3 65.2 + - + +
24E SER* 3.9 1.9 + - - -
25E ILE* 3.1 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ARG* 2.7 60.8 + - + +
19E TYR* 3.4 8.7 - - - +
21E VAL* 1.3 80.9 - - + +
23E HIS* 1.3 65.4 + - - +
25E ILE* 3.7 12.7 - - - +
26E THR* 3.1 25.1 - - + +
51F HEM 4.0 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TYR* 2.8 72.2 + + + +
20E TRP* 4.6 3.6 - - + +
22E ILE* 1.3 75.5 - - + +
24E SER* 1.3 53.3 + - - +
25E ILE 2.6 18.0 + - - -
26E THR* 3.0 20.2 - - + +
27E ILE* 3.0 31.9 + - + +
28E PRO* 3.6 4.0 - - - +
51F HEM 2.0 82.6 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TRP* 2.8 32.3 + - - +
21E VAL* 4.5 2.0 - - - -
22E ILE 3.5 0.6 - - - -
23E HIS* 1.3 69.1 - - - +
25E ILE* 1.3 64.1 + - - +
28E PRO* 4.3 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E VAL* 3.1 25.8 - - + +
22E ILE* 3.7 10.1 - - - +
23E HIS 2.6 6.9 + - - -
24E SER* 1.3 82.2 - - - +
26E THR* 1.3 57.2 + - + +
27E ILE 3.6 0.4 - - - -
28E PRO* 3.8 4.1 - - - +
29E ALA* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ILE* 3.1 21.3 - - + +
23E HIS* 3.0 29.3 - - - -
25E ILE* 1.3 78.6 - - + +
27E ILE* 1.3 73.1 + - - -
29E ALA* 3.0 6.6 - - - +
30E LEU* 2.9 29.2 + - - +
51F HEM 3.6 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TYR* 4.6 7.2 - - + +
20E TRP* 5.6 7.2 - - + -
23E HIS* 3.0 21.8 + - + +
26E THR* 1.3 86.3 + - - +
28E PRO* 1.3 76.1 - - + +
30E LEU* 3.0 3.6 + - - +
31E PHE* 2.9 19.6 + - + -
31F ILE* 3.5 21.6 - - + +
51F HEM 3.6 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E HIS 3.6 9.9 - - - +
24E SER* 4.3 9.2 - - - +
25E ILE* 3.8 9.6 - - - +
27E ILE* 1.3 98.8 - - + +
29E ALA* 1.3 52.4 + - - +
31E PHE* 3.4 9.4 - - + +
32E ILE* 2.8 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ILE* 2.8 26.1 + - + +
26E THR* 3.0 11.4 - - - +
28E PRO* 1.3 77.8 - - - +
30E LEU* 1.3 55.3 + - + +
32E ILE* 3.4 5.9 + - - +
33E ALA* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E THR 2.9 14.5 + - - +
27E ILE 3.4 6.5 - - - +
29E ALA* 1.3 78.2 - - + +
31E PHE* 1.3 62.8 + - - +
33E ALA* 2.9 10.8 + - + +
34E GLY* 2.9 22.5 + - - -
28F VAL* 3.4 55.6 - - + +
31F ILE* 3.8 10.1 - - + -
32F PHE* 4.0 17.4 - - + +
51F HEM 3.8 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ILE* 2.9 13.6 + - + +
28E PRO* 3.4 13.9 - - + +
30E LEU* 1.3 76.9 - - - +
32E ILE* 1.3 65.2 + - + +
35E TRP* 3.1 50.7 + + - +
31F ILE* 3.7 19.2 - - + +
34F LEU* 3.5 11.2 - - + -
35F GLY* 3.3 30.3 - - - -
38F ALA* 3.7 17.5 - - + -
24J ILE* 4.2 13.7 - - + -
27J LEU* 6.0 0.2 - - + -
----------------------------------------------------------
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 PRO* 2.8 33.6 + - + +
29E ALA* 4.0 4.5 - - - +
31E PHE* 1.3 81.3 - - + +
33E ALA* 1.3 64.9 + - - +
34E GLY 3.3 0.2 - - - -
35E TRP* 3.7 9.6 - - + +
36E LEU* 3.0 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ALA 2.7 20.4 + - - +
30E LEU* 2.9 14.3 + - + +
32E ILE* 1.3 79.6 - - - +
34E GLY* 1.3 61.4 + - - +
36E LEU* 3.5 9.5 + - - +
37E PHE* 3.4 14.0 + - - +
32F PHE* 3.9 13.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E LEU 2.9 10.3 + - - -
33E ALA* 1.3 71.4 - - - +
35E TRP* 1.3 61.8 + - - +
36E LEU 3.0 2.2 - - - -
37E PHE* 2.8 23.6 + - - +
38E VAL 3.3 4.5 + - - -
32F PHE* 3.2 40.7 - - - -
36F ALA* 3.7 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E PHE* 3.1 43.7 + + + +
32E ILE* 3.7 13.2 - - + +
33E ALA 3.4 0.4 - - - -
34E GLY* 1.3 77.2 - - - +
36E LEU* 1.3 66.2 + - + +
38E VAL 3.6 0.3 + - - -
39E SER* 2.8 45.9 + - - -
35F GLY 3.6 23.8 - - - +
38F ALA* 3.7 19.3 - - + -
39F ALA* 3.6 19.5 - - + +
42F PHE* 3.6 31.0 - + + -
27J LEU* 5.2 2.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
32E ILE* 3.0 30.0 + - + +
33E ALA* 3.7 10.3 - - - +
34E GLY 3.0 0.4 - - - -
35E TRP* 1.3 87.4 - - + +
37E PHE* 1.3 59.3 + - - +
38E VAL 3.1 2.5 - - - -
39E SER* 3.6 9.9 - - - +
40E THR* 2.6 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PHE* 3.8 29.4 - + - -
33E ALA 3.4 5.2 + - - +
34E GLY* 2.8 18.1 + - - +
36E LEU* 1.3 78.3 - - - +
38E VAL* 1.3 54.5 + - - +
42E LEU* 3.2 44.2 + - + -
43E ALA* 2.8 56.4 + - + -
46E VAL* 3.8 14.8 - - + -
47E PHE* 3.9 17.5 - + - -
32F PHE* 3.7 29.4 - + + -
36F ALA* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PHE* 4.2 8.1 - - + -
68D LEU* 4.0 8.3 - - + -
34E GLY 3.3 1.4 + - - -
35E TRP 4.0 4.9 - - - +
36E LEU 3.1 0.2 - - - -
37E PHE* 1.3 77.9 - - - +
39E SER* 1.3 59.4 + - - +
40E THR 3.2 0.2 - - - -
41E GLY* 2.7 28.1 + - - -
43E ALA* 4.3 4.5 - - - -
44E TYR* 5.0 4.6 - - + -
36F ALA* 3.3 41.7 - - + +
39F ALA* 4.0 8.7 - - + +
40F MET* 3.8 34.8 - - + +
43F ILE* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TRP* 2.8 38.9 + - - -
36E LEU* 3.6 15.0 - - - +
38E VAL* 1.3 79.7 - - - +
40E THR* 1.3 58.9 + - - +
41E GLY* 3.5 0.5 + - - -
39F ALA* 4.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LEU* 2.6 38.5 + - - +
37E PHE* 5.1 0.2 - - - -
39E SER* 1.3 73.0 - - - +
41E GLY* 1.3 57.8 + - - +
42E LEU* 3.9 21.1 - - + +
----------------------------------------------------------
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