Contacts of the helix formed by residues 26 - 49 (chain b) in PDB entry 3J9X
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 ASN 26 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22b ASN 3.6 2.2 + - - +
23b ALA 3.1 15.8 + - - +
24b PHE 3.0 1.6 + - - -
25b SER* 1.3 78.2 + - - +
27b PRO* 1.4 67.1 - - - +
28b THR* 2.9 24.2 + - - -
29b VAL* 2.7 37.2 + - + -
30b ALA* 2.8 11.5 + - - -
32c THR* 4.0 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27a PRO* 3.5 33.3 - - + +
28a THR* 5.5 1.3 - - + -
31a SER* 3.5 19.1 - - - +
25b SER 3.2 7.0 - - - +
26b ASN* 1.4 93.2 - - - +
28b THR* 1.3 61.0 + - - +
30b ALA* 4.0 2.8 - - + +
31b SER* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27a PRO* 5.7 0.4 - - - -
26b ASN* 2.8 15.2 + - - -
27b PRO* 1.3 74.3 - - - +
29b VAL* 1.3 61.5 + - - +
31b SER* 3.1 4.7 + - - -
32b THR* 2.5 47.5 + - - +
26c ASN* 4.8 4.3 - - - +
28c THR* 3.1 33.7 - - + +
29c VAL* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23b ALA 3.3 28.7 - - - +
24b PHE* 3.8 9.9 - - - -
26b ASN* 2.7 14.2 + - + +
28b THR* 1.3 70.5 - - - +
30b ALA* 1.3 66.5 + - - +
32b THR* 3.7 0.3 - - - -
33b ILE* 3.1 43.7 + - + +
28c THR 4.3 0.9 - - - +
29c VAL* 3.9 29.4 - - + +
32c THR* 3.8 31.4 - - + +
33c ILE* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30a ALA* 3.6 28.7 - - + -
34a LEU* 4.6 2.7 - - + -
24b PHE* 3.3 36.5 + - + +
25b SER 4.9 1.1 - - - -
26b ASN 2.8 11.3 + - - +
27b PRO* 4.0 4.3 - - + +
29b VAL* 1.3 78.9 - - - +
31b SER* 1.3 58.5 + - - +
33b ILE* 4.0 0.3 - - - +
34b LEU* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25a SER 3.5 23.1 + - - -
27a PRO* 3.5 24.7 - - - +
27b PRO 2.8 21.4 + - - -
28b THR* 3.1 7.8 + - - -
30b ALA* 1.3 77.4 - - - +
32b THR* 1.3 58.6 + - - +
34b LEU* 4.5 0.9 - - - +
35b SER* 2.6 42.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28b THR* 2.5 33.8 + - - +
29b VAL 3.7 3.8 - - - -
31b SER* 1.3 79.2 + - - +
33b ILE* 1.3 63.2 + - - +
35b SER* 3.2 3.5 + - - -
36b ASN* 3.1 34.4 + - - +
23c ALA* 3.6 34.3 - - + +
26c ASN* 4.0 15.6 + - + +
29c VAL* 3.7 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1747 T 5.7 2.2 - - - +
1668 T 3.7 38.1 - - - +
1678 A 4.7 6.7 - - - +
24b PHE* 4.2 14.1 - - + -
29b VAL* 3.1 34.6 + - + +
30b ALA 4.0 2.0 - - - +
32b THR* 1.3 79.0 - - - +
34b LEU* 1.3 58.8 + - - +
36b ASN* 3.1 3.3 + - - +
37b VAL* 3.0 29.9 + - + +
20c LYS* 4.0 23.3 - - + -
23c ALA* 3.8 21.8 - - + -
29c VAL* 4.9 8.3 - - + -
33c ILE* 5.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658 A 4.9 7.0 - - + -
1668 T 4.6 14.1 - - - +
21a PHE* 4.1 21.2 - - + -
24a PHE* 3.4 40.6 - - + +
25a SER* 3.9 26.2 - - - -
30a ALA* 4.5 0.2 - - + -
24b PHE* 4.0 22.0 - - + -
30b ALA* 2.9 27.7 + - + +
31b SER 4.3 0.2 - - - +
33b ILE* 1.3 78.1 - - - +
35b SER* 1.3 52.2 + - - +
37b VAL* 3.4 8.5 + - + +
38b SER* 2.6 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25a SER* 4.6 9.1 - - - -
31b SER* 2.6 27.6 + - - -
32b THR* 3.2 6.4 + - - -
34b LEU* 1.3 77.3 - - - +
36b ASN* 1.3 70.0 + - - +
38b SER* 3.4 20.2 + - - -
39b PRO* 4.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32b THR* 3.1 23.9 + - - +
33b ILE 3.1 4.9 + - - +
35b SER* 1.3 85.8 + - - +
37b VAL* 1.3 58.5 + - - +
38b SER 3.3 1.0 + - - -
39b PRO* 3.6 12.5 - - - +
40b VAL* 4.3 1.9 - - - +
19c ALA* 3.4 29.5 + - + +
22c ASN* 4.0 10.3 - - - +
23c ALA* 3.4 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658 A 4.1 20.9 - - - +
1668 T 3.9 6.7 - - - +
21a PHE* 4.6 9.0 - - + -
33b ILE* 3.0 21.3 + - + +
34b LEU* 3.5 17.3 - - + +
36b ASN* 1.3 75.1 - - - +
38b SER* 1.3 65.5 + - - +
39b PRO* 3.5 1.3 - - - -
40b VAL* 3.3 9.0 + - + -
41b ALA* 2.8 23.8 + - + +
16c LYS* 4.9 7.9 - - + -
19c ALA* 3.7 22.2 - - + -
20c LYS* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21a PHE* 3.5 22.5 - - - -
22a ASN* 5.5 2.5 + - - -
25a SER* 4.6 4.9 + - - -
34b LEU 2.6 20.1 + - - -
35b SER* 3.4 15.9 - - - -
36b ASN 3.3 0.2 - - - -
37b VAL* 1.3 81.1 - - - +
39b PRO* 1.4 73.3 - - - +
41b ALA* 2.9 10.9 + - - +
42b GLN* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 39 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35b SER 4.1 4.5 - - - +
36b ASN 3.6 11.7 - - - +
37b VAL 3.5 1.8 - - - -
38b SER* 1.4 97.4 - - - +
40b VAL* 1.3 68.4 + - + +
42b GLN* 3.4 20.2 + - - +
43b GLN* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658 A 4.8 1.3 - - - +
36b ASN 4.3 13.5 - - - +
37b VAL* 3.5 12.3 - - + +
38b SER 3.0 0.4 - - - -
39b PRO* 1.3 78.5 - - + +
41b ALA* 1.3 66.8 + - - +
43b GLN* 3.1 9.1 + - - +
44b ASN* 3.1 33.2 + - - +
12c GLN* 5.2 1.3 - - - +
15c ALA* 4.0 28.9 - - + +
16c LYS* 3.9 33.0 - - + +
19c ALA* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648 T 4.2 2.5 - - - +
1658 A 3.7 35.9 + - - -
17a TRP* 4.1 18.0 - - + -
21a PHE* 4.3 11.4 - - + -
37b VAL 2.8 13.7 + - - +
38b SER 3.3 8.7 - - - +
40b VAL* 1.3 75.7 - - - +
42b GLN* 1.3 57.5 + - - +
44b ASN* 3.1 2.5 + - - +
45b PHE* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14a TYR* 3.7 12.4 + - - +
17a TRP* 4.3 10.8 - - + -
18a GLN* 3.2 40.7 - - - +
21a PHE* 5.8 0.4 - - + -
22a ASN* 4.7 2.0 + - - -
38b SER* 3.0 20.4 + - - +
39b PRO* 3.5 30.2 - - - +
40b VAL 3.1 0.2 - - - -
41b ALA* 1.3 77.0 - - - +
43b GLN* 1.3 55.6 + - - +
45b PHE* 3.7 0.9 - - - +
46b GLN* 2.9 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39b PRO 3.1 8.9 + - - +
40b VAL* 3.1 11.7 + - - +
42b GLN* 1.3 81.7 - - - +
44b ASN* 1.3 61.4 + - - +
46b GLN* 3.7 14.3 + - - +
47b THR* 2.6 60.9 + - - +
12c GLN* 5.3 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1767 T 5.5 0.4 + - - -
1648 T 3.5 29.6 - - - +
1658 A 3.0 21.2 + - - -
40b VAL* 3.1 23.1 + - - +
41b ALA 3.1 3.3 + - - +
43b GLN* 1.3 76.7 - - - +
45b PHE* 1.3 66.2 + - - +
47b THR* 3.4 4.7 + - - -
48b ASN* 3.1 22.7 + - - +
8c ARG* 3.6 24.1 - - - +
12c GLN* 2.9 33.9 + - - +
16c LYS* 5.0 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877 A 5.2 5.4 - - - -
1638 A 4.6 10.5 - + - -
1648 T 3.6 23.5 - - - -
10a TYR* 4.1 1.8 - + - -
13a ARG* 4.5 5.8 - - + -
14a TYR* 3.4 43.5 - + + -
17a TRP* 3.5 59.9 - + + -
41b ALA 2.8 16.6 + - - +
42b GLN 3.7 3.6 - - - +
44b ASN* 1.3 76.5 - - - +
46b GLN* 1.3 64.0 + - - +
49b VAL* 3.0 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10a TYR* 3.3 21.7 + - - +
14a TYR* 2.9 39.2 + - + -
42b GLN* 2.9 33.5 + - - +
43b GLN* 3.7 15.7 + - - +
45b PHE* 1.3 77.4 - - - +
47b THR* 1.3 62.9 + - - +
50b PRO* 3.1 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43b GLN* 2.6 42.2 + - - +
44b ASN* 3.7 6.5 - - - -
45b PHE 3.2 0.2 - - - -
46b GLN* 1.3 80.4 - - - +
48b ASN* 1.3 74.0 + - - +
50b PRO* 3.7 6.2 - - - +
51b LYS* 3.4 23.0 - - - +
12c GLN* 4.6 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1638 A 3.8 20.2 - - - +
1648 T 3.1 20.4 + - - -
44b ASN 3.1 10.9 + - - +
47b THR* 1.3 87.0 - - - +
49b VAL* 1.3 62.9 + - - +
50b PRO* 3.4 1.8 - - - -
51b LYS* 3.0 34.2 + - + +
52b PHE* 3.1 27.5 - - + -
88b ASN* 4.9 4.7 + - - -
7c SER 3.9 14.4 + - - +
8c ARG* 3.4 15.0 - - - +
12c GLN* 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1638 A 3.9 28.7 - - + +
10a TYR* 3.8 10.3 - - + -
13a ARG* 3.7 26.9 + - - +
45b PHE* 3.0 64.1 + - + +
48b ASN* 1.3 70.9 - - - +
50b PRO* 1.4 61.0 - - + +
51b LYS 3.0 4.0 - - - -
52b PHE* 2.8 30.9 + - + +
53b THR 3.2 7.1 + - - -
----------------------------------------------------------
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