Contacts of the helix formed by residues 3 - 21 (chain A) in PDB entry 1JR5
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 LYS 3 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 3.4 8.1 - - - +
2A ASN* 1.3 92.5 + - - +
4A ASN* 1.3 67.3 + - - +
5A ILE* 3.2 22.7 - - + +
6A ASP* 3.0 24.3 + - - +
7A THR* 3.5 1.7 + - - -
44A HIS* 3.0 20.3 + - - -
65A ASP* 5.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 1.3 73.8 - - - +
5A ILE* 1.3 56.5 + - - +
6A ASP 2.9 0.5 + - - -
7A THR* 3.1 2.4 + - - -
8A VAL* 2.6 46.4 + - + +
44A HIS* 4.8 5.0 + - - -
56A LYS 4.8 0.5 - - - +
57A ILE* 2.5 49.9 + - + +
60A GLU* 3.0 33.0 + - - +
61A LEU* 3.4 8.5 - - + +
65A ASP* 3.7 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 3.7 28.3 - - + -
4A ASN* 1.3 76.3 - - - +
6A ASP* 1.3 65.8 + - - +
8A VAL* 3.9 4.4 - - - +
9A ARG* 2.7 42.3 + - + +
65A ASP* 2.6 55.9 + - - +
68A THR* 3.5 21.1 - - + -
69A LEU* 3.4 29.6 - - + +
1B MET* 5.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.0 68.4 - - + +
2A ASN 3.4 0.2 + - - -
3A LYS* 3.0 26.8 + - - +
4A ASN 2.9 1.6 + - - -
5A ILE* 1.3 83.0 - - - +
7A THR* 1.3 58.6 + - - +
8A VAL 3.0 4.0 - - - -
9A ARG* 3.0 13.3 - - - +
10A GLU* 3.0 32.8 + - - +
44A HIS* 5.2 0.4 - - - +
1B MET* 4.2 16.6 - - - +
6B ASP* 4.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS 3.5 1.8 + - - -
4A ASN 3.1 3.2 + - - -
6A ASP* 1.3 76.6 - - - +
8A VAL* 1.3 57.2 + - - +
10A GLU* 3.2 24.5 + - + +
11A ILE* 2.8 38.0 + - + +
42A VAL* 4.9 0.4 - - + -
43A THR 4.2 2.2 + - - +
44A HIS* 2.7 51.5 + - + +
49A LEU* 4.1 18.6 - - + -
57A ILE* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN* 2.6 35.8 + - + +
5A ILE* 3.6 7.6 - - - +
7A THR* 1.3 70.1 - - - +
9A ARG* 1.3 60.6 + - - +
10A GLU 2.9 0.7 - - - -
11A ILE* 2.9 7.7 + - + +
12A ILE* 2.7 44.5 + - + +
57A ILE* 3.2 33.0 - - + -
61A LEU* 4.1 16.4 - - + -
65A ASP* 4.8 0.9 - - + +
69A LEU* 5.1 9.2 - - + -
81A TYR* 4.6 21.1 - - + -
84A LEU* 5.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.8 0.2 - - - -
5A ILE* 2.7 31.2 + - + +
6A ASP* 3.0 17.9 - - - +
8A VAL* 1.3 73.3 - - - +
10A GLU* 1.3 75.8 + - - +
12A ILE* 3.2 14.6 - - - +
13A THR* 2.9 41.9 + - - +
14A VAL* 6.1 0.4 - - - +
69A LEU* 4.4 8.7 - - + -
73A PHE* 3.4 31.6 - - + -
1B MET* 2.9 30.2 - - + +
9B ARG* 2.8 37.5 - - - +
10B GLU* 2.6 41.2 + - - +
14B VAL* 5.8 0.6 - - - +
42B VAL* 3.3 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.0 5.0 - - - +
6A ASP 3.0 16.0 + - - +
7A THR* 3.2 26.3 - - - +
8A VAL 2.9 0.6 - - - -
9A ARG* 1.3 85.7 - - - +
11A ILE* 1.3 69.4 + - - +
12A ILE 3.2 0.3 + - - -
13A THR* 3.2 1.4 + - - -
14A VAL* 2.7 39.6 + - + +
42A VAL* 2.7 38.2 - - + +
43A THR 3.4 18.8 - - - +
9B ARG* 2.6 47.5 + - - +
73B PHE* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 2.8 24.9 - - + +
8A VAL* 2.9 12.6 + - + +
10A GLU* 1.3 79.2 - - + +
12A ILE* 1.3 62.6 + - - +
14A VAL* 3.1 7.9 - - - +
15A ALA* 3.0 28.6 + - - +
33A PHE* 3.2 25.7 - - + -
37A LEU* 3.4 23.8 - - + -
49A LEU* 3.3 29.4 - - + -
54A PHE* 3.7 30.3 - - + -
57A ILE* 4.5 7.0 - - + -
84A LEU* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 2.7 35.9 + - + +
9A ARG* 3.2 25.6 - - - +
11A ILE* 1.3 76.5 - - - +
13A THR* 1.3 62.7 + - - +
15A ALA* 3.7 1.5 - - - -
16A SER 2.8 19.8 + - - -
33A PHE* 5.2 0.4 - - - -
69A LEU* 3.8 4.3 - - + -
73A PHE* 3.7 16.6 - - + -
77A PHE* 3.5 29.4 - - + -
80A VAL* 2.9 24.8 - - + +
81A TYR* 3.1 44.2 - - + +
84A LEU* 3.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.9 30.0 + - - +
10A GLU 3.8 2.0 - - - -
12A ILE* 1.3 76.8 - - - +
14A VAL* 1.3 62.9 + - + +
16A SER* 2.8 24.9 + - - -
17A ILE* 2.8 9.7 + - - +
73A PHE* 3.6 17.7 - - - -
80A VAL* 4.9 1.1 - - - -
14B VAL* 3.4 28.9 - - + -
40B ILE* 3.8 13.5 - - + +
41B GLY 4.2 5.6 + - - +
42B VAL* 3.6 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 6.1 0.4 - - - +
10A GLU* 2.7 36.6 + - - +
11A ILE* 3.1 22.0 - - - +
13A THR* 1.3 72.7 - - + +
15A ALA* 1.3 55.0 + - - +
17A ILE* 2.6 29.3 + - - +
18A LEU 3.0 8.3 + - - -
36A PHE* 3.3 20.4 - - + -
37A LEU* 3.8 12.1 - - + -
40A ILE* 4.6 2.5 - - + -
42A VAL* 4.7 1.8 - - + -
9B ARG* 5.8 0.4 - - - +
13B THR* 3.4 26.9 - - + -
14B VAL* 4.3 8.1 - - + -
17B ILE* 3.0 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE 3.0 13.7 + - - +
12A ILE* 3.9 2.5 - - - +
14A VAL* 1.3 73.7 - - - +
16A SER* 1.3 55.4 + - - +
18A LEU* 3.0 5.0 - - + +
19A ILE* 3.0 8.1 + - - +
27A VAL* 2.8 35.4 - - + +
33A PHE* 3.0 49.6 - - + -
36A PHE* 3.2 12.3 - - + -
80A VAL* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE 2.8 17.7 + - - -
13A THR* 2.8 12.7 + - - -
15A ALA* 1.3 74.1 - - - +
17A ILE* 1.3 54.6 + - - +
19A ILE* 3.0 18.0 + - - +
20A LYS* 2.7 35.6 + - - +
80A VAL* 3.2 22.9 - - - +
40B ILE* 3.5 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR 2.8 19.7 + - - +
14A VAL* 2.6 14.9 + - - +
16A SER* 1.3 71.7 + - - +
18A LEU* 1.3 49.6 + - - +
20A LYS* 2.9 10.0 + - - +
21A PHE* 2.8 76.1 + - + -
14B VAL* 3.0 41.3 - - + -
17B ILE* 3.3 26.5 - - + -
36B PHE* 3.5 20.2 - - + -
40B ILE* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL 3.0 4.0 + - - -
15A ALA* 3.0 15.3 - - + +
17A ILE* 1.3 76.5 - - - +
19A ILE* 1.3 53.7 + - - +
21A PHE 2.9 11.6 + - - -
23A ARG* 2.6 61.2 + - + +
26A ILE* 3.0 39.5 - - + -
27A VAL* 3.3 11.0 - - + +
33A PHE* 5.5 0.7 - - - -
36A PHE* 3.1 54.1 - - + -
21B PHE* 3.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.0 5.4 + - - +
16A SER* 3.0 21.1 + - - +
18A LEU* 1.3 79.3 - - - +
20A LYS* 1.3 61.4 + - + +
22A SER* 3.3 11.8 + - - -
24A GLU* 3.1 41.4 - - + +
27A VAL* 3.1 36.5 - - + +
79A GLY 5.3 2.9 - - - +
80A VAL* 6.3 1.3 - - + -
83A TYR* 3.8 32.1 - - + -
87A TYR* 3.9 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER 2.7 16.6 + - - +
17A ILE* 3.2 11.7 - - - +
19A ILE* 1.3 71.7 - - + +
21A PHE* 1.3 107.4 + - + +
22A SER* 3.1 8.3 + - - -
18B LEU* 4.8 1.0 - - - +
26B ILE* 4.8 4.9 - - - +
36B PHE* 3.7 7.7 - - - -
39B GLU* 2.8 36.3 + - + +
40B ILE* 3.3 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 2.8 37.4 + - + +
18A LEU 2.9 0.8 + - - -
20A LYS* 1.3 114.8 - - + +
22A SER* 1.3 69.7 + - - +
23A ARG* 2.9 26.7 + - + -
18B LEU* 3.3 32.5 - - + -
21B PHE* 3.1 37.0 - + + -
23B ARG* 4.1 24.9 - - + -
26B ILE* 4.7 1.3 - - + -
36B PHE* 4.4 0.4 - + - -
----------------------------------------------------------
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