Contacts of the helix formed by residues 45 - 69 (chain A) in PDB entry 1JT6
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 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.2 6.5 - - - -
40A TYR* 6.1 0.4 - - + -
43A PHE* 2.8 14.6 + - - +
44A LYS* 1.3 88.0 - - + +
46A LYS* 1.3 67.4 + - - +
47A GLU* 3.1 26.3 + - - +
48A ASN* 3.0 24.7 + - - +
49A LEU* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.3 13.6 - - + -
20A TYR* 3.2 51.8 + - + +
21A ASN* 3.3 15.6 + - - +
23A THR 2.8 24.5 + - - +
24A THR 5.0 0.2 - - - -
25A THR* 4.6 15.7 - - + +
28A ILE* 5.1 6.1 - - + -
39A LEU* 5.5 2.0 - - - +
45A THR* 1.3 71.8 - - - +
47A GLU* 1.3 60.9 + - - +
49A LEU* 2.9 11.6 + - + +
50A PHE* 2.9 27.7 + - - +
800A SO4 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.2 8.7 + - - +
45A THR* 3.1 32.7 + - - +
46A LYS* 1.3 80.3 + - - +
48A ASN* 1.3 63.4 + - - +
50A PHE* 3.4 2.5 + - - +
51A LEU* 3.0 28.9 + - - +
102A PHE* 3.9 18.3 - - + -
106A TYR* 3.1 46.6 + - + +
112A ILE* 4.3 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 2.8 33.3 + - + +
44A LYS* 5.1 3.6 - - - +
45A THR* 3.0 17.3 + - - +
47A GLU* 1.3 75.5 - - - +
49A LEU* 1.3 65.9 + - - +
51A LEU* 3.2 10.7 + - - +
52A GLU* 2.9 24.0 + - - +
111A SER* 5.5 1.7 + - - -
112A ILE* 5.8 2.8 - - - +
115A LYS* 4.3 30.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.6 3.4 - - + -
8A LEU* 3.4 28.9 - - + -
11A ALA* 3.7 14.4 - - + -
15A PHE* 4.5 5.2 - - + -
28A ILE* 3.7 36.1 - - + -
39A LEU* 4.7 10.1 - - + -
43A PHE* 4.0 31.6 - - + +
45A THR 2.9 11.2 + - - +
46A LYS* 3.1 13.5 - - + +
48A ASN* 1.3 75.0 - - - +
50A PHE* 1.3 65.3 + - - +
52A GLU* 2.9 12.5 + - - +
53A ILE* 3.0 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.7 28.0 - + + -
20A TYR* 3.8 24.2 - + + -
46A LYS 2.9 11.2 + - - +
47A GLU 3.7 7.0 - - - +
49A LEU* 1.3 76.9 - - - +
51A LEU* 1.3 62.1 + - - +
53A ILE* 3.1 14.6 + - + +
54A LEU* 2.9 47.4 + - + +
95A LEU* 4.3 8.5 - - + -
98A ALA* 3.8 41.1 - - + -
99A ILE* 3.9 14.8 - - + -
102A PHE* 3.4 38.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 3.0 20.8 + - - +
48A ASN* 3.5 13.9 - - - +
50A PHE* 1.3 75.6 - - - +
52A GLU* 1.3 57.0 + - - +
54A LEU* 3.2 15.2 + - + +
55A ASN* 3.0 29.0 + - - +
102A PHE* 4.0 22.4 - - + -
112A ILE* 4.3 22.7 - - + -
115A LYS* 3.5 41.3 - - + -
116A MET* 4.0 18.4 - - + -
119A LEU* 4.3 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 5.1 10.1 + - - -
8A LEU* 3.8 13.3 - - + +
43A PHE* 3.5 30.3 - - + -
48A ASN* 2.9 13.4 + - - +
49A LEU 3.3 9.0 - - - +
51A LEU* 1.3 73.2 - - - +
53A ILE* 1.3 67.2 + - - +
55A ASN* 3.2 21.7 + - - +
56A ILE* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 24.2 - - + +
11A ALA* 3.8 16.4 - - + -
12A LYS* 3.9 20.4 - - + +
15A PHE* 3.5 38.4 - - + -
49A LEU* 3.0 18.1 + - + +
50A PHE* 3.1 11.0 + - + +
52A GLU* 1.3 77.0 - - - +
54A LEU* 1.3 64.7 + - + +
56A ILE* 3.1 9.2 + - + +
57A GLU* 2.9 23.9 + - + +
95A LEU* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 2.9 46.5 + - + +
51A LEU* 3.2 21.0 + - + +
53A ILE* 1.3 77.8 - - + +
55A ASN* 1.3 52.3 + - - +
57A GLU* 3.2 6.7 + - + +
58A GLU* 2.7 36.0 + - - +
95A LEU* 4.3 14.1 - - + -
99A ILE* 3.9 28.9 - - + -
102A PHE* 4.8 0.4 - - + -
116A MET* 4.7 7.9 - - + -
119A LEU* 3.6 15.4 - - + +
201A DEQ 3.8 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 3.0 13.7 + - - +
52A GLU* 3.2 28.6 + - - +
54A LEU* 1.3 76.5 - - - +
56A ILE* 1.3 64.6 + - + +
58A GLU* 3.2 2.9 + - - +
59A SER* 3.0 27.3 + - - -
119A LEU* 3.3 27.0 - - - +
122A LYS* 4.4 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 5.4 1.8 - - - +
8A LEU* 3.4 37.7 - - + -
52A GLU* 3.1 26.0 + - - +
53A ILE* 3.1 9.2 + - - +
55A ASN* 1.3 80.2 - - + +
57A GLU* 1.3 66.0 + - - +
59A SER* 3.1 10.3 + - - -
60A LYS* 2.9 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.3 39.9 + - - +
53A ILE* 2.9 20.8 + - + +
54A LEU* 3.2 10.1 + - + +
56A ILE* 1.3 83.8 - - - +
58A GLU* 1.3 62.1 + - - +
60A LYS* 3.2 10.1 + - - +
61A TRP 2.9 19.2 + - - -
93A TYR* 2.6 37.2 + - - +
95A LEU* 3.6 14.8 - - + -
201A DEQ 3.1 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 2.7 19.6 + - - +
55A ASN 3.7 4.5 - - - +
57A GLU* 1.3 71.8 - - - +
59A SER* 1.3 59.1 + - - +
61A TRP* 3.1 27.5 + - - +
62A GLN* 2.8 54.8 + - - +
119A LEU* 4.0 22.1 - - + +
122A LYS* 3.9 15.0 - - + -
123A TYR* 3.8 31.8 - - - +
201A DEQ 3.9 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 3.0 15.6 + - - -
56A ILE* 3.1 11.0 + - - -
58A GLU* 1.3 74.1 - - - +
60A LYS* 1.3 66.7 + - - +
62A GLN* 3.2 11.1 + - - +
63A GLU* 3.0 23.8 + - - +
122A LYS* 5.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 5.3 5.1 - - - +
56A ILE* 2.9 40.3 + - + +
57A GLU* 3.2 15.5 + - - +
59A SER* 1.3 76.5 - - - +
61A TRP* 1.3 58.7 + - - +
63A GLU* 3.3 18.1 + - + +
64A GLN* 2.9 38.0 + - - +
201A DEQ 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU 2.9 13.8 + - - +
58A GLU* 3.4 25.8 - - - +
60A LYS* 1.3 75.8 - - - +
62A GLN* 1.3 67.1 + - + +
64A GLN* 3.3 15.5 + - + +
65A TRP* 2.9 30.1 + + + +
82A TYR* 3.3 43.4 + + - -
85A LEU* 4.2 21.3 - - + -
86A SER* 4.1 18.6 - - - -
89A THR* 3.3 31.4 - - + -
123A TYR* 4.2 9.7 - + - -
201A DEQ 3.6 53.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 2.8 50.8 + - - +
59A SER* 3.2 8.8 + - - +
61A TRP* 1.3 80.7 - - + +
63A GLU* 1.3 52.8 + - - +
65A TRP* 3.0 10.4 + - + +
66A LYS* 2.8 36.0 + - - +
122A LYS* 3.4 31.8 + - - +
126A ALA* 6.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER 3.0 16.6 + - - +
60A LYS* 3.3 23.3 - - + +
62A GLN* 1.3 75.3 - - - +
64A GLN* 1.3 78.3 + - - +
66A LYS* 3.3 13.8 + - + +
67A LYS* 3.2 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 2.9 31.7 + - - +
61A TRP* 3.6 15.6 - - + +
63A GLU* 1.3 92.3 + - - +
65A TRP* 1.3 58.2 + - - +
67A LYS* 3.2 9.0 + - - +
68A GLU* 2.9 30.1 + - - +
89A THR* 5.9 2.3 - - - +
201A DEQ 4.5 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 2.9 19.8 + + + +
62A GLN* 3.5 12.3 - - + +
64A GLN* 1.3 75.0 - - - +
66A LYS* 1.3 60.4 + - - +
68A GLU* 4.1 8.1 - - + +
69A GLN* 2.8 82.7 + - + +
78A LYS* 3.6 31.6 - - + -
81A LEU* 3.8 25.1 - - + -
82A TYR* 3.4 46.9 - + + -
85A LEU* 4.0 11.2 - - + -
126A ALA* 4.0 20.2 + - + +
130A ILE* 4.1 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN 2.8 19.3 + - - +
63A GLU* 3.5 12.8 - - + +
65A TRP* 1.3 74.0 - - - +
67A LYS* 1.3 59.6 + - - +
69A GLN* 3.5 23.8 - - - +
70A ILE* 3.9 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 3.2 22.2 + - - +
64A GLN* 3.2 11.6 + - - +
65A TRP 3.1 0.4 - - - -
66A LYS* 1.3 78.4 - - - +
68A GLU* 1.3 65.4 + - - +
70A ILE* 4.0 17.6 + - + +
71A LYS* 5.0 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN 2.9 16.5 + - - +
65A TRP* 3.0 9.6 + - + +
67A LYS* 1.3 79.0 - - - +
69A GLN* 1.3 62.0 + - - +
70A ILE 3.0 5.2 - - - -
71A LYS* 3.0 62.1 + - - +
81A LEU* 4.0 15.4 - - + +
85A LEU* 3.7 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 2.8 77.5 + - + +
66A LYS* 3.5 21.9 - - - +
68A GLU* 1.3 73.1 - - - +
70A ILE* 1.3 59.1 + - + +
71A LYS 3.0 0.2 - - - -
72A ALA* 2.7 36.3 + - - +
78A LYS* 3.7 25.4 + - + +
81A LEU* 4.5 2.5 - - - -
129A VAL* 5.4 7.5 - - - +
130A ILE* 6.0 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