Contacts of the helix formed by residues 44 - 69 (chain G) in PDB entry 5JRE
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 ASP 44 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G SER* 2.9 13.4 + - - +
42G ARG* 3.1 41.8 + - + +
43G GLU* 1.3 73.4 - - - +
45G TYR* 1.3 56.7 + - - +
46G LYS* 3.6 9.5 + - - +
47G SER* 2.7 35.0 + - - -
48G ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G MET* 3.6 43.2 + - + -
43G GLU* 3.2 49.0 + - + +
44G ASP* 1.3 71.4 - - - +
46G LYS* 1.3 60.4 + - - +
48G ALA* 3.7 3.8 - - + -
49G ASP* 2.9 43.4 + - - +
93G ILE* 3.8 17.8 - - + +
94G LYS* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ASP* 3.3 8.4 + - - +
45G TYR* 1.3 79.4 - - - +
47G SER* 1.3 62.6 + - - +
49G ASP* 3.5 5.8 + - - +
50G LYS* 3.3 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G SER* 4.1 5.4 - - - -
42G ARG* 4.4 4.3 + - - -
44G ASP* 2.7 33.1 + - - -
46G LYS* 1.3 76.3 - - - +
48G ALA* 1.3 67.8 + - - +
50G LYS* 3.2 12.2 + - - +
51G TYR* 3.0 45.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.2 14.9 - - + +
39G SER* 3.2 23.0 + - - +
40G MET* 3.5 31.6 - - - +
44G ASP 3.0 15.2 + - - +
45G TYR* 3.7 7.0 - - + +
47G SER* 1.3 77.1 - - - +
49G ASP* 1.3 58.0 + - - +
51G TYR* 3.3 1.8 + - - -
52G LYS* 2.8 27.3 + - - +
90G TYR* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G TYR* 2.9 28.4 + - - +
46G LYS* 3.9 5.8 - - - +
47G SER 3.3 0.2 - - - -
48G ALA* 1.3 74.4 - - - +
50G LYS* 1.3 62.7 + - - +
52G LYS* 3.8 5.8 - - - +
53G GLU* 3.1 24.9 + - - +
90G TYR* 2.7 32.7 + - - -
94G LYS* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LYS* 3.3 41.3 + - + +
47G SER* 3.2 14.0 + - - +
49G ASP* 1.3 77.8 - - - +
51G TYR* 1.3 65.7 + - + +
53G GLU* 3.3 8.8 + - - +
54G GLU* 3.1 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LYS* 4.3 12.2 + - - -
32G LEU* 3.8 24.2 - - + +
35G SER* 3.7 43.1 + - - -
36G LEU* 4.0 16.2 - - + +
39G SER* 4.0 6.1 - - - -
47G SER* 3.0 41.7 + - - +
48G ALA 3.7 3.4 - - - +
50G LYS* 1.3 80.0 - - + +
52G LYS* 1.3 58.0 + - - +
54G GLU* 3.4 14.3 + - - +
55G LEU* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.9 22.3 - - + +
48G ALA 2.8 20.6 + - - +
49G ASP* 3.8 6.5 - - - +
50G LYS 3.3 0.2 - - - -
51G TYR* 1.3 72.9 - - - +
53G GLU* 1.3 57.7 + - - +
55G LEU* 3.8 1.9 - - - +
56G THR* 2.7 48.2 + - - +
87G LEU* 4.5 12.8 - - + -
90G TYR* 3.4 44.3 + - + +
91G TYR* 3.4 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ASP 3.1 17.9 + - - +
50G LYS* 3.6 7.1 - - - +
51G TYR 3.3 0.2 - - - -
52G LYS* 1.3 78.4 - - - +
54G GLU* 1.3 62.9 + - + +
56G THR* 3.4 4.5 + - - -
57G ASN* 3.1 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 4.0 27.5 - - + +
50G LYS* 3.1 22.8 + - - +
51G TYR* 3.8 17.3 - - - +
53G GLU* 1.3 78.3 - - + +
55G LEU* 1.3 64.2 + - - +
57G ASN* 3.3 8.9 + - - +
58G LEU* 3.0 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G MET* 3.6 42.6 - - + +
32G LEU* 4.1 14.7 - - + +
33G SER* 3.5 29.6 - - - +
36G LEU* 4.0 11.2 - - + -
51G TYR 2.8 18.8 + - - +
52G LYS 3.8 3.4 - - - +
54G GLU* 1.3 76.8 - - - +
56G THR* 1.3 58.9 + - - +
58G LEU* 3.3 2.4 + - - +
59G ALA* 2.9 28.1 + - - +
83G TYR* 3.8 18.6 - - + -
86G ALA* 4.2 3.4 - - + -
87G LEU* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LYS* 2.7 32.3 + - - +
53G GLU* 3.8 5.4 - - - -
55G LEU* 1.3 75.9 - - - +
57G ASN* 1.3 61.0 + - - +
59G ALA* 3.3 2.4 + - - +
60G LYS* 3.0 37.4 + - + +
83G TYR* 4.2 18.2 + - - +
87G LEU* 4.0 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G GLU* 3.1 38.1 + - - +
54G GLU* 3.6 8.0 - - - +
56G THR* 1.3 75.7 - - - +
58G LEU* 1.3 65.3 + - + +
60G LYS* 3.3 10.3 + - - +
61G THR* 3.1 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ARG* 3.7 22.7 - - + +
28G ARG* 3.9 31.4 - - + +
29G MET* 3.8 22.4 - - + -
32G LEU* 3.7 25.8 - - + -
54G GLU 3.0 15.3 + - - +
55G LEU 3.7 6.7 - - - +
57G ASN* 1.3 75.3 - - + +
59G ALA* 1.3 59.8 + - - +
61G THR* 3.2 8.5 + - - +
62G GLN* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G MET* 3.7 19.7 - - + +
55G LEU 2.9 18.0 + - - +
56G THR 3.5 5.2 - - - +
58G LEU* 1.3 75.8 - - - +
60G LYS* 1.3 58.9 + - + +
62G GLN* 3.3 1.4 + - - +
63G ILE* 2.8 38.7 + - + +
80G LEU* 4.3 2.0 - - + -
83G TYR* 3.6 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G THR* 3.0 23.7 + - + +
57G ASN* 3.5 11.9 - - - +
58G LEU 3.3 0.2 - - - -
59G ALA* 1.3 76.2 - - - +
61G THR* 1.3 61.7 + - - +
63G ILE* 3.5 8.5 + - + +
64G GLU* 3.2 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ARG* 3.8 29.2 - - - +
57G ASN 3.1 12.7 + - - -
58G LEU* 3.6 11.2 - - + +
60G LYS* 1.3 75.6 - - - +
62G GLN* 1.3 63.2 + - - +
64G GLU* 2.9 33.6 - - + +
65G GLU* 3.0 14.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ILE* 3.1 46.1 + - - +
25G ARG* 2.8 40.5 + - - +
26G SER* 3.5 16.2 - - - +
29G MET* 3.9 15.5 - - - -
58G LEU 2.8 20.5 + - - +
59G ALA* 3.7 4.0 - - - +
61G THR* 1.3 72.9 - - - +
63G ILE* 1.3 65.3 + - - +
65G GLU* 3.2 1.0 + - - +
66G LEU* 2.9 34.1 + - + +
76G GLY* 3.8 11.4 + - - +
80G LEU* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ALA* 2.8 30.2 + - + +
60G LYS* 3.8 8.3 - - + +
62G GLN* 1.3 76.3 - - - +
64G GLU* 1.3 63.5 + - - +
66G LEU* 3.5 5.3 + - - +
67G LYS* 3.2 21.4 + - + +
80G LEU* 3.8 27.8 - - + -
83G TYR* 4.8 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G LYS 3.2 13.8 + - - +
61G THR* 2.9 33.1 - - - +
63G ILE* 1.3 76.9 - - - +
65G GLU* 1.3 79.3 + - - +
67G LYS* 3.4 9.6 - - - +
68G LYS* 3.3 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G LYS* 3.3 35.3 - - - +
21G GLU* 4.4 4.5 - - - +
22G ILE* 4.4 13.0 - - + +
25G ARG* 3.8 25.2 + - - +
61G THR* 3.0 26.4 + - + +
62G GLN 3.7 3.8 - - - +
64G GLU* 1.3 94.1 - - - +
66G LEU* 1.3 61.7 + - - +
68G LYS* 3.2 18.0 + - - +
69G TYR* 2.9 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ILE* 3.8 27.4 - - + -
62G GLN* 2.9 21.4 + - + +
63G ILE* 4.0 4.5 - - - +
65G GLU* 1.3 73.4 - - - +
67G LYS* 1.3 66.6 + - - +
69G TYR 3.3 2.4 - - - -
70G PRO* 3.2 26.7 - - - +
72G PHE 3.4 27.1 - - - +
73G TYR* 3.9 39.6 - - + +
76G GLY* 4.3 7.4 - - - -
77G PHE* 4.9 0.4 - - - +
80G LEU* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ILE* 3.2 12.1 + - + +
64G GLU* 3.4 13.2 - - - +
66G LEU* 1.3 80.7 - - - +
68G LYS* 1.3 66.0 + - + +
69G TYR 3.5 0.2 + - - -
70G PRO* 3.6 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLU* 3.3 33.2 + - - +
65G GLU* 3.2 18.7 + - - +
67G LYS* 1.3 82.3 - - + +
69G TYR* 1.3 90.4 + - + +
70G PRO* 3.4 6.8 - - - +
71G MET* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LYS* 2.8 32.5 + - - -
15G LEU* 3.6 26.9 - - + -
18G LYS* 3.5 47.4 - - + -
22G ILE* 4.4 6.7 - - + +
65G GLU* 2.9 33.1 + - - +
66G LEU* 3.3 8.6 - - - +
67G LYS 3.3 0.2 - - - -
68G LYS* 1.3 106.1 - - + +
70G PRO* 1.4 59.0 - - - +
71G MET* 3.2 8.7 - - - -
72G PHE* 2.9 41.2 + - + +
73G TYR 3.9 2.3 + - - -
----------------------------------------------------------
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