Contacts of the helix formed by residues 13 - 30 (chain s) in PDB entry 5JPQ
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 THR 13 (chain s).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12s LEU* 1.3 77.0 + - - +
14s LYS* 1.3 75.3 + - + +
15s ILE* 3.1 28.5 - - + -
16s GLU* 2.7 28.3 + - - +
17s GLU* 2.6 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 14 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13s THR* 1.3 79.4 - - + +
15s ILE* 1.3 65.8 + - + +
17s GLU* 3.1 19.7 + - - +
18s GLN* 3.0 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13s THR* 2.8 29.4 + - + -
14s LYS* 1.3 76.7 - - + +
16s GLU* 1.3 65.9 + - + +
17s GLU 3.2 0.3 + - - -
18s GLN* 3.3 16.6 + - - +
19s VAL* 2.9 30.8 + - + +
45s VAL* 4.2 8.1 - - + +
47s GLU* 3.0 39.0 - - + +
61s VAL* 3.7 37.5 - - + -
90s GLN* 5.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6s PHE* 3.8 20.9 - - + -
8s LYS* 3.5 29.1 + - - -
11s SER 4.1 0.7 - - - +
12s LEU* 3.5 19.2 - - + +
13s THR* 2.7 40.7 + - - +
15s ILE* 1.3 73.5 - - + +
17s GLU* 1.3 61.0 + - - +
19s VAL* 3.4 9.4 - - - +
20s GLY* 3.0 18.9 + - - -
44s GLN* 3.7 7.1 - - - +
45s VAL* 3.1 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2s ALA 4.8 0.7 + - - -
12s LEU* 3.4 36.2 + - + +
13s THR 2.6 22.6 + - - +
14s LYS* 3.1 26.7 - - - +
16s GLU* 1.3 70.1 - - - +
18s GLN* 1.3 67.4 + - + +
20s GLY* 2.8 12.3 + - - -
21s SER* 3.1 14.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14s LYS* 3.0 30.5 + - - +
15s ILE* 3.6 14.7 - - - +
17s GLU* 1.3 76.0 - - + +
19s VAL* 1.3 52.6 + - - +
21s SER* 3.2 8.4 + - - -
22s ALA* 2.7 39.5 + - - +
88s LEU* 3.5 28.2 - - + +
90s GLN* 5.1 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6s PHE* 5.3 1.1 - - + -
15s ILE* 2.9 25.8 + - + +
16s GLU* 3.4 11.4 - - - +
18s GLN* 1.3 78.1 - - + +
20s GLY* 1.3 57.5 + - - +
22s ALA* 3.4 6.5 - - + +
23s LEU* 2.9 46.6 + - + +
42s LEU* 4.6 9.2 - - + -
45s VAL* 4.2 29.6 - - + -
61s VAL* 5.3 1.8 - - + -
63s ILE* 4.6 12.6 - - + -
84s LEU* 5.6 5.4 - - + -
88s LEU* 4.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2s ALA 3.4 21.3 - - - -
5s LYS* 4.9 3.7 - - - +
6s PHE* 4.7 9.2 - - - -
12s LEU* 5.2 0.7 - - - -
16s GLU 3.0 10.3 + - - -
17s GLU* 2.8 9.6 + - - -
19s VAL* 1.3 77.4 - - - +
21s SER* 1.3 59.0 + - - -
23s LEU* 3.2 8.6 + - - +
24s VAL* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2s ALA 3.5 10.4 - - - +
17s GLU 3.1 10.9 + - - -
18s GLN* 3.2 12.8 + - - -
20s GLY* 1.3 71.3 - - - +
22s ALA* 1.3 56.9 + - - +
24s VAL* 3.2 7.2 + - - +
25s GLU* 2.7 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18s GLN 2.7 23.1 + - - +
19s VAL* 3.4 8.3 - - - +
21s SER* 1.3 78.1 + - - +
23s LEU* 1.3 58.9 + - - +
25s GLU* 3.0 31.5 - - - +
26s LEU* 3.3 15.2 + - - +
84s LEU* 4.1 18.8 - - + +
87s LYS* 4.8 8.2 - - + +
88s LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5s LYS* 3.9 23.8 - - + +
19s VAL* 2.9 31.1 + - + +
20s GLY* 3.6 6.7 - - - +
22s ALA* 1.3 73.5 - - - +
24s VAL* 1.3 65.5 + - - +
25s GLU 2.9 2.4 + - - -
26s LEU* 3.0 15.4 + - + +
27s GLN* 3.4 11.4 + - - +
37s LEU* 3.6 28.5 - - + +
40s ILE* 5.0 0.7 - - + -
42s LEU* 3.4 37.7 - - + -
63s ILE* 5.6 1.8 - - + -
80s LEU* 4.2 10.5 - - + -
84s LEU* 4.0 27.1 - - + -
94s PHE* 5.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2s ALA* 3.7 28.5 - - + +
5s LYS* 4.3 15.0 - - + +
20s GLY 2.9 18.1 + - - +
21s SER* 3.6 7.9 - - - +
23s LEU* 1.3 75.9 - - - +
25s GLU* 1.3 58.7 + - - +
27s GLN* 3.0 27.7 - - - +
28s ASN* 2.6 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21s SER* 2.7 23.0 + - - +
22s ALA* 3.0 22.4 + - - +
24s VAL* 1.3 76.0 - - - +
26s LEU* 1.3 58.3 + - - +
28s ASN* 3.1 10.3 + - - +
29s THR* 2.9 34.2 + - - +
87s LYS* 3.5 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22s ALA 3.5 9.9 - - - +
23s LEU* 3.0 8.7 + - - +
25s GLU* 1.3 81.0 - - - +
27s GLN* 1.3 57.9 + - - +
30s HIS* 2.9 55.9 + - + +
33s LEU* 4.1 7.6 - - + +
37s LEU* 3.9 13.9 - - + -
80s LEU* 4.3 11.7 - - + -
83s GLU* 3.5 27.4 - - + -
84s LEU* 3.7 32.3 - - + +
87s LYS* 3.1 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5s LYS* 3.1 29.9 + - - +
23s LEU 3.4 8.0 + - - +
24s VAL* 3.0 35.5 + - - +
26s LEU* 1.3 75.5 - - - +
28s ASN* 1.3 67.4 + - - +
30s HIS 3.7 12.0 - - - +
31s PRO* 5.3 0.7 - - - +
33s LEU 4.5 1.3 - - - -
34s LYS* 3.8 30.0 - - - +
37s LEU* 3.6 24.1 - - + +
38s GLU* 3.9 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24s VAL* 2.6 38.1 + - - +
25s GLU* 3.1 8.4 + - - +
27s GLN* 1.3 86.8 + - - +
29s THR* 1.3 67.4 + - - +
30s HIS 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25s GLU* 2.9 18.9 + - - +
28s ASN* 1.3 80.7 - - - +
30s HIS* 1.3 90.3 + - + +
31s PRO* 3.8 6.6 - - - +
87s LYS* 3.6 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26s LEU* 2.9 60.2 + - + +
27s GLN 3.7 11.7 - - - +
28s ASN 5.0 1.3 - - - -
29s THR* 1.3 94.5 + - + +
31s PRO* 1.3 68.5 - - + +
32s ASP* 3.5 19.2 + - - +
33s LEU* 3.8 12.0 + - + -
34s LYS 3.7 7.3 + - - -
83s GLU* 3.6 22.1 + - - -
87s LYS* 3.7 7.0 + - - -
----------------------------------------------------------
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