Contacts of the helix formed by residues 15 - 39 (chain Q) in PDB entry 1TQE
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 ARG 15 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C A 6.3 3.4 - - + -
13Q ASP* 2.9 23.3 + - - +
14Q GLN* 1.3 86.4 + - + +
16Q ASN* 1.3 59.9 + - - +
18Q GLN* 3.1 18.7 + - - +
19Q VAL* 3.1 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 16 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D A 5.1 5.5 - - - +
14D G 4.0 25.4 + - - +
11Q ILE* 3.0 32.8 - - + +
13Q ASP* 2.7 29.5 + - + +
15Q ARG* 1.3 68.7 - - - +
17Q ARG* 1.3 57.8 + - - +
18Q GLN 3.0 5.2 - - - -
19Q VAL* 3.9 10.3 - - - +
20Q THR* 3.0 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P LEU 3.9 13.7 - - - +
39P CYS* 3.9 21.6 + - - +
10Q ARG* 2.8 42.8 - - - +
11Q ILE* 2.9 42.1 + - + +
12Q LEU 3.4 21.0 + - - -
13Q ASP 2.8 12.6 + - - +
14Q GLN* 3.6 29.1 - - - +
15Q ARG 3.2 0.2 - - - -
16Q ASN* 1.3 75.4 - - - +
18Q GLN* 1.3 57.5 + - - +
20Q THR 4.3 2.0 - - - -
21Q PHE* 3.7 18.2 + - - +
50Q SER* 5.1 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C A 3.0 41.5 - - - +
2C A 5.7 0.6 + - - -
14Q GLN* 3.4 18.1 + - + +
15Q ARG* 3.1 5.8 + - - +
16Q ASN 3.0 0.6 - - - -
17Q ARG* 1.3 79.5 - - - +
19Q VAL* 1.3 64.6 + - + +
20Q THR 3.3 1.3 - - - -
21Q PHE* 3.9 13.0 - - - +
22Q THR* 3.4 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C A 5.8 12.8 - - + +
2C A 5.5 13.5 - - + +
14D G 6.1 1.8 - - - +
15Q ARG* 3.1 21.0 + - + +
16Q ASN* 3.9 10.8 - - - +
18Q GLN* 1.3 79.1 - - + +
20Q THR* 1.3 60.8 + - - +
22Q THR* 3.5 4.2 + - - -
23Q LYS* 3.1 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D A 3.5 27.8 + - - +
38P LEU* 4.6 4.0 - - + -
39P CYS* 4.1 6.5 - - - -
11Q ILE* 3.6 25.5 - - + +
16Q ASN* 3.0 25.4 + - - -
19Q VAL* 1.3 77.8 - - - +
21Q PHE* 1.3 66.7 + - - +
23Q LYS* 4.4 6.1 - - - -
24Q ARG* 2.9 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 21 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P LEU* 3.9 11.6 - - + +
39P CYS* 3.3 40.4 - - + -
41P CYS* 3.7 26.9 - - + -
17Q ARG 3.7 11.9 + - - +
18Q GLN* 3.7 16.1 + - - +
19Q VAL 3.5 0.4 - - - -
20Q THR* 1.3 77.5 - - - +
22Q THR* 1.3 68.2 + - - +
25Q LYS* 2.9 66.3 + - + +
47Q ILE* 4.1 15.5 - - + -
49Q ASN* 4.4 12.6 - - + -
55Q PHE* 3.9 28.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C A 5.4 7.5 + - - +
18Q GLN* 3.4 24.3 + - - -
19Q VAL* 3.8 7.9 - - - +
20Q THR 3.2 0.4 - - - -
21Q PHE* 1.3 83.0 - - - +
23Q LYS* 1.3 72.2 + - + +
25Q LYS* 3.9 13.5 + - - +
26Q PHE* 3.3 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C G 4.4 6.8 + - - -
5C C 4.6 2.4 - - - +
12D T 4.3 20.3 + - + +
13D A 3.2 28.5 + - + +
14D G 2.8 33.3 + - - -
15D C 4.8 1.4 - - - +
19Q VAL* 3.1 34.7 + - + +
20Q THR* 3.3 6.9 + - - +
22Q THR* 1.3 84.8 - - + +
24Q ARG* 1.3 65.5 + - + +
26Q PHE* 3.3 7.0 + - - +
27Q GLY* 3.2 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D T 3.7 35.5 + - - +
13D A 3.3 32.2 + - - +
31P LYS* 4.4 11.1 + - - +
34P GLU* 2.8 44.3 + - - +
35P LEU* 4.0 22.8 - - + +
38P LEU* 3.2 30.6 - - - +
6Q ILE* 4.7 5.5 - - - +
8Q ILE* 6.0 0.4 - - - +
20Q THR* 2.9 30.4 + - + +
23Q LYS* 1.3 69.2 - - + +
25Q LYS* 1.3 68.5 + - - +
26Q PHE 2.9 1.8 - - - -
27Q GLY* 2.6 15.5 + - - +
28Q LEU* 2.7 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P LEU* 3.5 19.7 - - + +
77P GLU* 3.3 28.5 + - - +
79P ARG* 5.8 0.2 - - - +
21Q PHE* 2.9 45.4 + - + +
22Q THR* 3.9 15.8 + - - +
24Q ARG* 1.3 71.1 - - - +
26Q PHE* 1.3 75.2 + - - +
28Q LEU* 3.3 2.3 + - - +
29Q MET* 3.0 38.0 + - - +
47Q ILE* 3.7 17.3 - - + -
55Q PHE* 3.6 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P ARG* 3.2 38.1 - - - -
84P ILE* 4.7 18.6 - - + -
87P THR* 4.6 17.9 - - + -
88P LEU* 5.2 10.1 - - + -
22Q THR* 3.3 8.9 + - + +
23Q LYS* 3.3 11.1 + - - +
24Q ARG 2.7 4.0 + - - -
25Q LYS* 1.3 85.2 - - - +
27Q GLY* 1.3 60.6 + - - +
29Q MET* 3.1 9.9 + - + +
30Q LYS* 2.7 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D A 5.2 5.1 - - - +
12D T 3.9 20.0 - - - -
31P LYS* 5.3 2.5 - - - -
23Q LYS 3.2 4.8 + - - -
24Q ARG 2.6 11.5 + - - -
26Q PHE* 1.3 79.1 - - - +
28Q LEU* 1.3 61.0 + - - -
30Q LYS* 3.0 13.5 + - - +
31Q LYS* 2.8 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D T 5.2 1.8 + - - -
28P LEU* 3.6 20.6 - - + +
31P LYS* 3.5 20.2 - - + +
32P ALA* 3.1 41.3 - - + +
35P LEU* 3.8 24.0 - - + -
43P ILE* 4.6 3.4 - - + -
45P LEU* 6.0 0.4 - - + -
24Q ARG 2.7 14.1 + - - +
25Q LYS* 3.4 9.4 - - - +
27Q GLY* 1.3 73.0 - - - +
29Q MET* 1.3 64.6 + - - +
31Q LYS* 3.0 5.4 + - - +
32Q ALA* 2.9 19.4 + - - +
45Q LEU* 3.8 31.6 - - + -
47Q ILE* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 29 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P GLU* 4.6 7.2 - - - +
79P ARG* 3.8 24.9 - - + -
84P ILE* 3.1 22.6 - - + +
25Q LYS* 3.0 34.7 + - + +
26Q PHE* 3.6 9.9 - - + +
28Q LEU* 1.3 76.2 - - - +
30Q LYS* 1.3 63.8 + - - +
32Q ALA* 3.3 9.7 + - - +
33Q TYR 2.8 19.4 + - - -
45Q LEU* 4.0 15.9 - - + +
47Q ILE* 4.9 4.5 - - + -
55Q PHE* 4.8 2.2 - - + -
56Q GLN* 2.9 46.4 - - - +
57Q TYR* 3.3 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D A 2.6 44.5 + - - +
84P ILE* 4.0 11.9 - - + +
88P LEU* 4.1 27.0 - - + +
26Q PHE* 2.7 36.0 + - + +
27Q GLY* 3.0 16.4 + - - +
29Q MET* 1.3 75.5 - - - +
31Q LYS* 1.3 58.0 + - - +
33Q TYR* 3.1 15.2 + - + +
34Q GLU* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C A 3.5 19.5 + - - -
12C T 3.3 29.2 + - - +
10D A 4.6 3.2 + - - -
11D A 4.0 37.2 + - - +
24P ARG* 4.3 7.5 + - - +
27P GLY 5.3 0.9 - - - -
28P LEU* 3.4 26.7 - - + +
31P LYS* 4.2 21.5 - - + +
27Q GLY 2.8 15.4 + - - +
28Q LEU* 3.6 4.5 - - - +
30Q LYS* 1.3 72.7 - - - +
32Q ALA* 1.3 71.7 + - - +
34Q GLU* 2.9 22.6 + - - +
35Q LEU* 2.7 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P LEU* 3.2 24.5 - - + +
45P LEU* 5.5 0.4 - - + -
28Q LEU 2.9 13.3 + - - +
29Q MET* 3.3 11.7 - - - +
31Q LYS* 1.3 79.9 - - - +
33Q TYR* 1.3 63.4 + - - +
35Q LEU* 2.9 2.6 + - - +
36Q SER* 2.7 20.3 + - - -
43Q ILE* 3.7 10.2 - - + +
45Q LEU* 4.6 7.2 - - + -
57Q TYR* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 33 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ILE* 4.1 23.9 + - + +
81P ASN* 3.7 25.4 - - + +
84P ILE* 3.5 30.3 - - + -
85P LEU* 3.2 41.0 - - + +
88P LEU* 4.1 17.6 - - + +
29Q MET 2.8 13.2 + - - +
30Q LYS* 3.2 15.7 - - + +
32Q ALA* 1.3 77.5 - - - +
34Q GLU* 1.3 91.5 + - + -
36Q SER* 3.1 3.9 - - - -
37Q VAL* 3.0 36.3 + - + +
57Q TYR* 3.0 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D A 5.3 0.6 - - - +
11D A 4.1 8.3 + - - -
8P ILE* 4.3 24.0 - - + +
24P ARG* 2.8 35.9 + - - +
30Q LYS* 2.8 44.6 + - + +
31Q LYS* 3.4 16.7 + - - +
33Q TYR* 1.3 89.5 - - + +
35Q LEU* 1.3 68.0 + - - +
37Q VAL* 2.9 2.9 + - - -
38Q LEU* 2.8 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P PHE* 3.9 17.9 - - + +
24P ARG* 4.2 24.2 - - + +
25P LYS* 3.6 28.5 - - + +
28P LEU* 3.7 22.4 - - + -
47P ILE* 4.0 15.5 - - + -
31Q LYS 2.7 16.0 + - - +
32Q ALA* 3.4 7.2 - - - +
34Q GLU* 1.3 71.2 - - - +
36Q SER* 1.3 63.2 + - - +
38Q LEU* 4.5 7.0 - - - -
39Q CYS* 3.1 41.3 + - - -
41Q CYS* 3.6 8.8 - - - -
43Q ILE* 4.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P ASN* 3.4 10.7 + - - -
32Q ALA 2.7 15.2 + - - -
33Q TYR 3.1 10.8 - - - -
34Q GLU 2.9 0.4 + - - -
35Q LEU* 1.3 73.5 - - - +
37Q VAL* 1.3 56.0 + - - -
40Q ASP* 3.0 10.0 + - - -
41Q CYS* 3.0 40.1 + - - +
43Q ILE* 3.9 7.8 - - - +
57Q TYR* 3.7 13.2 - - - -
59Q SER* 3.1 25.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ILE* 3.6 34.3 - - + +
9P SER* 3.8 9.2 - - - -
10P ARG* 3.5 11.7 + - - +
81P ASN* 4.6 9.2 - - + +
85P LEU* 5.9 2.9 - - + -
33Q TYR* 3.0 34.2 + - + +
34Q GLU 2.9 6.7 + - - -
36Q SER* 1.3 75.0 - - - +
38Q LEU* 1.3 70.3 + - - +
40Q ASP* 3.2 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P ILE* 4.3 13.0 - - + -
7P GLN 4.0 20.6 - - - +
8P ILE* 4.1 17.7 - - + -
9P SER 4.2 8.3 - - - +
10P ARG* 3.2 2.6 - - - -
11P ILE* 2.9 49.7 + - + +
17P ARG* 4.1 1.0 - - - +
20P THR* 4.6 3.4 - - + -
24P ARG* 3.3 51.4 - - - +
34Q GLU* 2.8 24.4 + - + +
35Q LEU* 4.1 1.8 - - - +
37Q VAL* 1.3 77.0 - - - +
39Q CYS* 1.3 66.5 + - - +
40Q ASP 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 39 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P ILE* 4.9 0.9 - - - -
17P ARG* 4.0 25.7 + - + +
20P THR* 4.2 9.9 - - - -
21P PHE* 3.4 57.5 - - + -
49P ASN* 5.6 1.4 - - - +
50P SER* 4.7 4.0 + - - -
35Q LEU* 3.1 22.4 + - - +
36Q SER 3.9 0.2 - - - -
38Q LEU* 1.3 85.7 - - - +
40Q ASP* 1.3 72.4 + - - +
41Q CYS* 3.3 5.8 + - - +
----------------------------------------------------------
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