Contacts of the helix formed by residues 37 - 55 (chain N) in PDB entry 2J28
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 37 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278B C 5.3 0.3 + - - -
1650B A 3.9 16.1 + - - +
1651B G 3.5 24.1 + - - +
36N THR* 1.3 80.4 - - - +
38N LEU* 1.3 58.0 + - - +
39N PRO* 3.4 16.8 - - + -
40N LYS* 3.1 19.1 + - - +
41N ALA* 2.7 34.7 + - - +
103N ARG* 4.0 13.6 + - - +
108N ALA* 5.0 1.6 - - + -
109N PRO* 3.5 24.8 + - + +
110N MET 3.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2817B U 4.4 26.5 - - - +
37N THR* 1.3 71.8 - - - +
39N PRO* 1.3 77.7 - - + +
41N ALA* 2.9 21.2 + - + +
42N LYS* 3.0 15.4 + - + +
97N ILE* 4.0 26.9 - - + -
99N LYS* 4.5 17.3 - - + +
109N PRO* 3.8 18.4 - - + -
110N MET 3.1 11.5 + - - +
111N ALA* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 39 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651B G 3.6 40.2 - - - +
1652B A 4.5 1.8 - - - +
9N GLN* 3.5 27.4 - - - +
37N THR* 3.4 13.2 - - + -
38N LEU* 1.3 101.4 - - + +
40N LYS* 1.3 61.0 - - - +
42N LYS* 3.7 4.5 + - + +
43N GLU* 3.4 26.9 + - - +
109N PRO* 3.9 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277B G 3.1 34.9 + - - +
1278B C 4.9 2.0 + - - -
1650B A 4.5 8.1 + - - -
1651B G 3.2 25.7 + - - +
9N GLN* 5.3 1.3 - - - +
11N ASN* 4.7 11.9 - - - +
12N ARG* 4.2 20.7 - - - +
20N MET* 4.7 7.0 - - + -
21N PHE* 4.2 4.4 - - + -
24N MET* 3.5 22.9 - - + -
36N THR* 3.3 22.8 - - + +
37N THR* 3.1 20.5 + - - +
39N PRO* 1.3 78.6 - - - +
41N ALA* 1.3 51.6 + - - +
43N GLU* 3.1 8.7 + - - +
44N LEU* 2.7 35.5 + - - +
103N ARG* 4.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N THR* 4.9 4.2 - - - -
37N THR 2.7 18.5 + - - +
38N LEU* 2.9 16.3 + - - +
40N LYS* 1.3 71.5 - - - +
42N LYS* 1.3 57.8 + - - +
44N LEU* 2.6 35.8 + - - +
45N ARG* 3.4 11.5 + - - +
97N ILE* 4.5 3.6 - - + -
110N MET 4.9 0.2 - - - +
111N ALA* 4.4 3.6 - - + -
113N ILE* 3.3 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2818B U 3.5 26.9 - - - +
2837B A 5.0 2.7 - - - +
2838B G 2.9 51.3 + - - +
2881B U 5.4 3.4 + - - -
8N ARG* 5.6 0.7 + - - -
38N LEU* 3.0 16.9 + - + +
39N PRO* 4.3 4.3 - - + +
41N ALA* 1.3 77.0 - - - +
43N GLU* 1.3 64.0 + - - +
45N ARG* 3.1 38.7 - - - +
46N ARG* 4.3 1.9 + - - +
97N ILE* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N ARG* 3.0 45.9 + - + +
9N GLN* 2.9 48.9 - - + +
21N PHE* 3.9 26.6 - - + -
39N PRO 3.4 10.4 + - - +
40N LYS* 3.1 10.7 + - - +
41N ALA 2.8 1.6 + - - -
42N LYS* 1.3 82.5 - - - +
44N LEU* 1.3 56.9 + - - +
45N ARG 2.8 11.5 + - - -
46N ARG* 3.2 22.8 + - - +
47N VAL* 3.9 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N PHE* 4.4 6.7 - - + -
24N MET* 3.4 39.7 - - + -
25N ALA 3.5 15.3 - - - +
28N LEU* 4.4 19.7 - - + -
34N ILE* 5.4 4.7 - - + -
36N THR* 5.1 4.9 - - - +
40N LYS 2.7 12.6 + - - +
41N ALA* 2.6 19.4 + - - +
43N GLU* 1.3 70.9 - - - +
45N ARG* 1.3 59.6 + - - +
47N VAL* 3.0 32.1 - - + +
48N VAL* 3.0 28.5 + - + +
113N ILE* 4.5 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2838B G 3.6 15.3 - - - +
2839B G 4.8 0.4 - - - -
2881B U 6.2 0.2 - - - -
28N LEU* 5.5 0.2 - - - +
41N ALA 4.1 4.9 + - - -
42N LYS* 3.1 43.3 - - - +
43N GLU 2.8 2.2 + - - -
44N LEU* 1.3 77.5 + - - +
46N ARG* 1.3 53.5 + - - +
47N VAL 2.7 15.8 + - - -
48N VAL* 3.0 0.8 + - - -
49N GLU* 2.8 42.0 + - - +
95N THR* 3.2 45.8 + - - +
96N ARG 3.1 5.9 + - - -
97N ILE* 3.0 23.7 - - - +
113N ILE* 2.9 52.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2690B U 5.1 11.5 + - - -
2691B C 5.3 7.1 + - - -
2838B G 4.8 1.3 + - - +
2839B G 3.9 22.0 - - - +
2873B A 5.9 0.2 - - - +
8N ARG* 3.0 75.1 - - - +
21N PHE* 5.0 13.5 - - - -
42N LYS 4.3 1.1 + - - +
43N GLU* 3.2 10.7 + - - +
45N ARG* 1.3 78.5 - - - +
47N VAL* 1.3 76.0 + - - +
50N PRO* 3.0 22.3 - - - +
69N ARG* 5.7 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N PHE* 4.3 19.3 - - + -
25N ALA* 4.3 8.7 - - + -
43N GLU 4.0 2.0 - - - +
44N LEU* 3.0 47.8 - - + +
45N ARG 2.7 4.8 + - - -
46N ARG* 1.3 98.3 - - - +
48N VAL* 1.3 63.5 + - + +
49N GLU 3.4 0.2 - - - -
50N PRO* 3.5 10.5 - - - +
51N LEU* 3.0 24.4 - - + +
69N ARG* 4.0 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N ALA* 3.6 15.5 - - + +
28N LEU* 3.7 28.9 - - + -
29N VAL* 5.4 4.7 - - + -
44N LEU* 3.0 42.0 + - + +
45N ARG 3.0 1.6 + - - +
47N VAL* 1.3 74.7 - - - +
49N GLU* 1.3 66.9 + - - +
51N LEU* 3.0 12.7 + - + +
52N ILE* 2.9 39.4 + - + +
94N TYR 5.5 0.2 - - - +
95N THR* 4.3 15.7 - - + -
115N LEU* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2838B G 4.5 2.8 + - - +
2839B G 3.0 57.7 + - - +
2840B C 3.8 2.7 - - - +
45N ARG* 2.8 27.6 + - - +
48N VAL* 1.3 71.8 - - - +
50N PRO* 1.3 72.8 - - + +
52N ILE* 2.9 9.8 + - + +
53N THR* 2.8 25.5 + - - +
92N GLY* 5.3 0.4 - - - -
93N GLY* 4.1 7.3 + - - +
94N TYR* 4.2 13.8 - - + +
95N THR* 2.6 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 50 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2839B G 4.3 2.9 - - - +
2840B C 3.6 17.3 - - - +
46N ARG* 3.0 30.5 - - - +
47N VAL* 3.5 10.1 - - - +
49N GLU* 1.3 91.8 - - + +
51N LEU* 1.3 51.6 + - + +
53N THR* 3.5 2.8 - - - -
54N LEU* 2.6 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N ALA* 3.9 24.0 - - + +
29N VAL* 5.6 4.0 - - + -
47N VAL* 3.0 22.4 - - + +
48N VAL* 3.0 17.4 + - + +
49N GLU 3.0 0.6 - - - -
50N PRO* 1.3 75.3 - - + +
52N ILE* 1.3 68.3 + - + +
54N LEU* 3.2 19.5 + - + +
55N ALA* 3.7 5.5 + - - +
66N ALA* 5.1 11.7 - - + +
69N ARG* 3.9 32.8 - - + -
70N THR* 4.7 17.9 - - - +
75N ILE* 5.7 1.8 - - + -
79N LEU* 3.1 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 4.9 2.7 - - + -
48N VAL* 2.9 36.8 + - + +
49N GLU* 3.5 11.0 - - + +
51N LEU* 1.3 77.9 - - + +
53N THR* 1.3 66.8 + - - +
55N ALA* 3.6 18.2 + - - +
79N LEU* 3.9 7.6 - - + -
83N LEU* 3.9 34.3 - - + +
84N GLY* 4.7 10.6 - - - +
87N PHE* 5.0 5.8 - - + -
91N ALA 5.8 3.1 - - - +
94N TYR* 3.6 44.6 - - + +
115N LEU* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2840B C 3.0 42.8 + - - +
2841B C 4.1 21.5 - - - +
49N GLU* 2.8 15.1 + - - +
50N PRO* 3.8 4.3 - - - -
52N ILE* 1.3 80.5 - - - +
54N LEU* 1.3 62.1 + - - +
55N ALA 3.0 12.1 + - - +
56N LYS* 4.6 4.9 + - - +
91N ALA 5.3 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N PRO 2.6 22.5 + - - +
51N LEU* 3.2 12.0 + - + +
53N THR* 1.3 72.0 - - - +
55N ALA* 1.3 57.8 + - + +
56N LYS* 3.5 12.0 + - - +
62N ASN* 3.4 27.0 + - + +
65N LEU* 3.8 36.1 - - + -
66N ALA* 3.5 15.3 - - + +
69N ARG* 6.4 1.1 - - + -
79N LEU* 6.2 0.7 - - + -
80N PHE* 3.3 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N LEU 3.7 5.3 + - - +
52N ILE 3.6 15.6 + - - +
53N THR 3.0 6.1 - - - +
54N LEU* 1.3 77.0 - - + +
56N LYS* 1.3 58.2 + - - +
79N LEU* 3.1 34.5 - - + +
80N PHE* 3.8 22.7 - - + +
84N GLY* 4.0 12.9 - - - +
85N PRO* 5.8 0.2 - - - +
88N ALA* 6.0 2.6 - - - +
----------------------------------------------------------
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