Contacts of the helix formed by residues 37 - 66 (chain m) 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 VAL 37 (chain m).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127 T 3.9 21.1 - - - +
1137 A 3.9 5.6 - - - +
16l LYS* 4.7 10.1 - - + -
19l ALA* 3.7 18.2 - - + -
20l LYS* 3.6 30.7 - - + -
33m ILE 3.0 20.7 + - - +
34m LEU* 3.5 15.7 - - + +
36m ASN* 1.3 76.3 - - - +
38m SER* 1.3 68.5 + - - +
39m PRO* 3.5 1.6 - - - -
40m VAL* 3.3 9.1 + - + +
41m ALA* 2.9 20.1 + - + +
21n PHE* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34m LEU 2.6 23.6 + - - -
35m SER* 3.3 15.5 - - - -
36m ASN 3.3 0.2 - - - -
37m VAL* 1.3 81.0 - - - +
39m PRO* 1.4 73.3 - - - +
41m ALA* 2.9 10.4 + - - +
42m GLN* 2.9 27.2 + - - +
21n PHE* 3.5 21.1 - - - -
22n ASN* 5.5 1.9 + - - -
25n SER* 4.7 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 39 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35m SER 4.0 4.3 - - - +
36m ASN 3.6 12.3 - - - +
37m VAL 3.5 2.0 - - - -
38m SER* 1.4 96.7 - - - +
40m VAL* 1.3 68.2 + - + +
42m GLN* 3.5 19.3 + - - +
43m GLN* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127 T 4.8 1.1 - - - +
12l GLN* 5.0 1.8 - - + +
15l ALA* 4.1 29.6 - - + +
16l LYS* 3.9 32.8 - - + +
19l ALA* 4.5 4.3 - - + -
36m ASN 4.3 13.2 - - - +
37m VAL* 3.5 13.5 - - + +
38m SER 3.0 0.8 + - - -
39m PRO* 1.3 78.3 - - + +
41m ALA* 1.3 66.9 + - - +
43m GLN* 3.1 10.1 + - + +
44m ASN* 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117 A 3.9 4.6 - - - +
1127 T 3.5 39.7 + - - +
37m VAL 2.9 18.1 + - - +
38m SER 3.4 3.8 - - - +
40m VAL* 1.3 76.6 - - - +
42m GLN* 1.3 58.4 + - - +
44m ASN* 3.1 2.9 + - - +
45m PHE* 2.8 31.2 + - - +
17n TRP* 4.1 15.4 - - + -
21n PHE* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38m SER* 2.9 21.3 + - - +
39m PRO* 3.5 30.1 - - - +
40m VAL 3.1 0.2 - - - -
41m ALA* 1.3 77.5 - - - +
43m GLN* 1.3 62.8 + - - +
45m PHE* 3.3 1.2 + - - +
46m GLN* 2.9 35.9 + - - +
14n TYR* 3.9 9.1 + - - +
17n TRP* 4.2 11.9 - - + -
18n GLN* 3.2 42.5 - - - +
21n PHE* 5.6 1.1 - - + -
22n ASN* 4.6 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12l GLN* 5.3 8.1 - - + +
39m PRO 3.1 11.2 + - - +
40m VAL* 3.3 12.1 - - - +
42m GLN* 1.3 79.5 - - - +
44m ASN* 1.3 59.3 + - - +
46m GLN* 3.4 13.3 + - - +
47m THR* 2.6 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117 A 3.6 24.6 - - - +
1127 T 2.9 20.0 + - - -
8l ARG* 3.7 24.8 - - - +
12l GLN* 2.9 34.9 + - - +
16l LYS* 5.5 3.6 - - - +
40m VAL* 3.1 21.4 + - - +
41m ALA 3.1 7.4 + - - +
43m GLN* 1.3 76.9 - - - +
45m PHE* 1.3 65.6 + - - +
47m THR* 3.4 5.0 + - - -
48m ASN* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107 T 4.5 10.3 - - - -
1117 A 3.5 28.0 - - - -
2408 T 5.3 7.0 - - - -
41m ALA 2.8 16.8 + - - +
42m GLN 3.7 3.4 - - - +
44m ASN* 1.3 77.0 - - - +
46m GLN* 1.3 59.3 + - - +
49m VAL* 2.9 69.6 + - + +
10n TYR* 5.1 0.9 - + - -
13n ARG* 4.4 5.6 - - + -
14n TYR* 3.5 44.0 - + + -
17n TRP* 3.5 56.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42m GLN* 2.9 27.5 + - - +
43m GLN* 3.8 13.4 + - - +
45m PHE* 1.3 80.3 - - - +
47m THR* 1.3 63.5 + - - +
50m PRO* 3.1 24.7 - - - +
10n TYR* 5.2 12.1 + - + +
14n TYR* 3.4 48.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12l GLN* 4.9 12.4 + - - +
43m GLN* 2.6 47.0 + - - +
44m ASN* 3.7 6.9 - - - -
45m PHE 3.2 0.2 - - - -
46m GLN* 1.3 80.2 - - - +
48m ASN* 1.3 71.1 + - - +
50m PRO* 4.3 2.4 - - - +
51m LYS* 3.4 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107 T 3.8 18.4 - - - +
1117 A 3.0 20.8 + - - -
7l SER* 4.5 7.9 + - - -
8l ARG* 3.8 12.7 - - - +
12l GLN* 5.5 3.6 - - - +
44m ASN* 3.1 10.1 + - - +
47m THR* 1.3 87.7 - - - +
49m VAL* 1.3 68.1 + - - +
50m PRO* 3.4 1.3 - - - -
51m LYS* 2.9 50.2 + - + +
52m PHE* 3.4 12.4 - - + -
88m ASN* 4.9 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107 T 3.6 33.9 - - + +
45m PHE* 2.9 56.8 + - + +
48m ASN* 1.3 74.2 - - - +
50m PRO* 1.3 63.9 - - + +
52m PHE* 2.9 26.1 + - - +
53m THR* 3.0 12.6 + - - +
10n TYR* 4.6 6.7 - - + -
13n ARG* 3.8 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 50 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45m PHE 3.8 0.9 - - - +
46m GLN 3.1 25.6 - - - +
47m THR 4.2 2.0 - - - +
48m ASN 3.4 3.1 - - - +
49m VAL* 1.3 98.5 - - + +
51m LYS* 1.3 60.6 + - + +
53m THR* 3.8 1.1 - - - +
54m SER* 3.2 23.9 + - - -
10n TYR* 3.7 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47m THR* 3.4 24.5 + - - +
48m ASN* 2.9 36.4 + - - +
49m VAL 3.0 0.4 - - - -
50m PRO* 1.3 77.9 - - + +
52m PHE* 1.3 63.0 + - + +
54m SER* 2.9 19.1 + - - -
55m VAL* 3.3 12.6 - - - +
84m ALA* 5.5 0.7 - - - +
88m ASN* 3.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097 A 3.7 17.3 - - + +
1107 T 3.4 39.9 - - - +
48m ASN* 3.4 19.3 - - + -
49m VAL* 2.9 7.2 + - + +
51m LYS* 1.3 77.2 - - + +
53m THR* 1.3 66.6 + - - +
54m SER 3.2 1.3 - - - -
55m VAL* 3.1 6.7 + - - +
56m ASN* 2.9 27.9 + - - +
81m LEU* 3.7 30.0 - - + +
84m ALA* 3.6 25.8 - - + -
85m ARG* 3.6 14.8 - - - -
88m ASN* 3.3 31.4 - - - -
13n ARG* 4.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49m VAL* 3.0 8.3 + - - +
50m PRO 3.4 6.0 + - - -
52m PHE* 1.3 76.5 - - - +
54m SER* 1.3 62.7 + - - +
56m ASN* 3.1 9.4 + - + +
57m GLU* 3.0 23.2 + - + +
8n ARG 4.7 5.2 - - - +
9n SER* 4.2 6.7 - - - -
10n TYR* 3.1 46.4 - - + +
13n ARG* 2.7 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50m PRO 3.2 10.9 + - - -
51m LYS* 2.9 22.3 + - - -
53m THR* 1.3 78.1 - - - +
55m VAL* 1.3 56.7 + - - +
57m GLU* 3.4 7.6 + - - +
58m ASN* 3.0 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51m LYS 3.3 17.9 - - - +
52m PHE* 3.1 9.6 + - - +
53m THR 3.1 0.2 - - - -
54m SER* 1.3 76.9 + - - +
56m ASN* 1.3 61.8 + - - +
58m ASN* 4.9 2.5 - - - +
59m VAL* 2.8 52.9 + - + +
77m GLN* 5.2 0.7 - - - +
80m GLY 4.1 13.7 - - - +
81m LEU* 4.3 10.1 - - + -
84m ALA* 4.0 20.4 - - + -
125m ILE* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2418 A 4.8 4.2 + - - +
2428 T 4.1 36.6 + - - +
52m PHE* 2.9 17.2 + - - +
53m THR* 3.1 9.3 + - + +
55m VAL* 1.3 75.5 - - - +
57m GLU* 1.3 57.2 + - - +
60m SER* 2.9 31.4 + - - -
77m GLN* 3.1 20.9 + - - +
81m LEU* 3.3 30.3 - - - +
13n ARG* 4.0 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53m THR* 3.0 14.6 + - + +
54m SER* 3.5 11.4 - - - +
56m ASN* 1.3 75.1 - - - +
58m ASN* 1.3 75.1 + - - +
60m SER* 3.2 8.4 + - - -
61m ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 58 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54m SER* 3.0 23.4 + - - +
55m VAL* 4.1 2.6 - - - +
57m GLU* 1.3 88.5 - - - +
59m VAL* 1.3 63.1 + - + +
61m ALA* 3.2 9.9 + - - +
62m VAL* 3.2 24.8 + - - +
124m ILE* 3.7 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55m VAL* 2.8 37.3 + - + +
58m ASN* 1.3 73.6 - - + +
60m SER* 1.3 66.5 + - - +
62m VAL* 3.1 9.9 + - - +
63m LEU* 2.9 33.5 + - + +
76m TYR 4.3 1.3 - - - +
77m GLN* 3.3 32.5 - - - +
80m GLY* 4.7 1.6 - - - -
121m VAL* 4.0 38.4 - - + +
124m ILE* 5.5 3.1 - - + -
125m ILE* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2428 T 4.9 0.4 - - - -
2438 A 3.4 9.7 + - - -
56m ASN 2.9 22.3 + - - -
57m GLU* 3.4 9.6 - - - -
59m VAL* 1.3 75.9 - - - +
61m ALA* 1.3 64.4 + - - +
63m LEU* 3.1 2.6 + - - -
64m THR* 3.0 12.9 + - - -
73m ARG* 2.7 41.4 + - - +
77m GLN* 3.4 12.3 - - - +
89o ARG 4.7 3.3 + - - -
90o ILE 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57m GLU* 3.0 15.6 + - - +
58m ASN* 3.4 13.2 - - - +
59m VAL 3.2 0.2 - - - -
60m SER* 1.3 77.1 - - - +
62m VAL* 1.3 63.6 + - + +
64m THR* 3.2 8.1 + - - -
65m GLN* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58m ASN 3.2 12.8 + - - +
59m VAL* 3.1 12.5 + - + +
61m ALA* 1.3 78.5 - - + +
63m LEU* 1.3 68.9 + - + +
65m GLN* 2.9 24.6 + - - +
66m TYR* 3.0 39.3 + - + -
117m VAL* 5.3 1.1 - - + +
120m ALA* 4.0 17.7 - - + +
121m VAL* 4.8 6.5 - - + +
124m ILE* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59m VAL* 2.9 34.1 + - + +
60m SER* 3.1 7.6 + - - +
62m VAL* 1.3 78.9 - - + +
64m THR* 1.3 60.5 + - - +
66m TYR* 3.2 2.6 + - - +
67m GLY 3.0 4.2 + - - -
68m ILE* 2.9 43.3 + - + +
73m ARG* 3.5 48.9 - - + +
76m TYR* 3.6 34.5 - - + -
77m GLN* 4.0 10.1 - - + +
117m VAL* 4.1 11.4 - - + -
121m VAL* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60m SER 3.0 6.1 + - - -
61m ALA* 3.6 11.1 - - - -
63m LEU* 1.3 77.4 - - - +
65m GLN* 1.3 62.1 + - + +
67m GLY 3.1 9.7 + - - -
73m ARG* 3.0 20.8 + - - +
90o ILE* 2.6 34.0 + - + +
91o GLY 3.8 6.5 - - - +
92o SER 3.3 28.0 - - - +
93o GLY* 4.6 1.3 - - - -
94o PRO* 3.3 4.4 - - + +
95o ALA* 3.3 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61m ALA* 3.1 18.8 + - - +
62m VAL* 2.9 17.6 + - - +
64m THR* 1.3 78.6 - - + +
66m TYR* 1.3 65.8 + - + +
67m GLY 3.3 0.4 - - - -
94o PRO* 3.4 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62m VAL* 3.0 34.8 + - + +
63m LEU* 3.2 6.7 + - - +
65m GLN* 1.3 85.0 - - + +
67m GLY* 1.3 61.6 + - - +
68m ILE* 3.2 21.6 + - + +
116m GLN* 2.9 43.4 + - - -
117m VAL* 4.1 17.0 - - + -
120m ALA* 3.5 27.2 - - + +
94o PRO* 4.6 0.7 - - - -
----------------------------------------------------------
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