Contacts of the helix formed by residues 37 - 65 (chain C) in PDB entry 1JGC
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 LEU 37 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN 3.0 12.6 + - - +
35C TRP* 4.1 25.4 - - + +
36C GLY* 1.3 81.8 - - - +
38C ALA* 1.3 65.7 + - - +
40C MET* 3.1 27.6 + - + -
41C ALA* 2.9 20.3 + - - +
83C PRO* 3.6 32.5 - - + -
149C PHE* 6.0 0.7 - - + -
150C ALA* 3.6 40.8 - - + +
153C ASN* 3.2 15.3 - - + +
154C ALA* 4.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLU* 3.8 23.2 + - - +
36C GLY 3.3 6.2 + - - +
37C LEU* 1.3 74.7 - - - +
39C LYS* 1.3 58.7 + - + +
41C ALA* 3.1 4.8 + - - +
42C LYS* 2.9 49.7 + - - +
153C ASN 3.5 1.8 + - - -
155C ALA* 3.6 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA* 1.3 75.7 - - + +
40C MET* 1.3 66.9 + - - +
42C LYS* 3.7 14.9 + - + +
43C LYS* 3.6 17.2 + - - +
152C LEU 3.7 21.2 + - - +
153C ASN* 3.2 23.2 + - - +
154C ALA 3.7 19.7 + - - +
155C ALA* 5.2 4.3 - - - +
156C PRO* 5.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 3.2 37.2 - - - +
37C LEU* 3.1 37.8 + - + +
39C LYS* 1.3 78.8 - - - +
41C ALA* 1.3 64.0 + - - +
43C LYS* 3.3 8.4 + - - +
44C SER* 3.3 14.8 + - - +
83C PRO* 3.6 29.2 - - - +
86C THR* 3.8 0.4 - - - +
87C LEU* 3.7 28.0 - - + -
149C PHE* 4.0 23.8 - - + -
153C ASN* 3.7 17.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 3.3 31.1 - - + +
32C GLN* 3.4 11.2 + - + -
33C GLU* 3.4 30.3 - - - +
37C LEU 2.9 12.9 + - - +
38C ALA* 3.3 9.9 - - - +
40C MET* 1.3 79.1 - - - +
42C LYS* 1.3 61.9 + - - +
44C SER* 3.1 4.2 + - - -
45C ARG 3.0 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 5.0 2.7 - - + -
33C GLU* 5.3 4.7 - - - +
38C ALA* 2.9 35.5 + - - +
39C LYS* 4.1 12.4 - - + +
40C MET 3.4 0.4 - - - -
41C ALA* 1.3 77.0 - - + +
43C LYS* 1.3 61.4 + - - +
45C ARG* 3.3 8.8 + - - +
46C GLU* 3.1 34.5 + - - +
160C ALA* 5.8 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LYS 3.6 9.4 + - - +
40C MET* 3.3 11.5 + - - +
41C ALA 3.2 0.4 - - - -
42C LYS* 1.3 80.0 - - - +
44C SER* 1.3 62.1 + - - +
46C GLU* 3.2 27.0 + - - +
47C GLU* 3.0 44.0 + - - +
50C GLU* 4.9 8.1 + - - -
130C HIS* 6.0 2.7 - - - -
133C PHE* 3.7 50.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.7 24.8 - - - +
28C HIS* 4.1 5.4 - - - +
29C PHE* 3.8 6.7 - - - -
32C GLN* 2.7 35.4 + - - -
40C MET* 3.3 2.5 + - - +
41C ALA 3.1 6.1 + - - -
43C LYS* 1.3 79.3 - - - +
45C ARG* 1.3 61.8 + - - +
47C GLU* 3.3 13.6 + - - +
48C SER* 3.0 24.6 + - - -
90C ASP* 4.8 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 3.5 33.7 - - + -
29C PHE* 3.3 47.1 - - + +
30C ARG* 5.9 1.2 - - - +
41C ALA 3.0 11.8 + - - +
42C LYS* 3.6 12.3 - - - +
43C LYS 3.2 0.2 - - - -
44C SER* 1.3 74.7 - - - +
46C GLU* 1.3 64.2 + - + +
48C SER* 3.3 5.7 + - - -
49C ILE* 3.0 40.2 + - - +
202C HEM 3.5 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS* 3.1 26.1 + - - +
43C LYS* 3.2 31.5 + - + +
45C ARG* 1.3 78.4 - - + +
47C GLU* 1.3 57.4 + - + +
49C ILE* 3.2 9.6 + - - +
50C GLU* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.5 40.2 + - + -
43C LYS* 3.0 42.7 + - - +
44C SER* 3.8 10.9 + - - +
46C GLU* 1.3 75.2 - - - +
48C SER* 1.3 63.1 + - - +
50C GLU* 3.1 13.9 + - - +
51C GLU* 3.0 27.0 + - - +
90C ASP* 5.1 1.7 - - - +
130C HIS* 4.5 27.5 - - + +
133C PHE* 3.9 22.1 - - - -
134C LEU* 4.5 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 2.9 22.2 + - - +
25C TYR* 3.5 26.8 - - - +
26C TRP* 3.3 19.4 - - - -
44C SER 3.0 12.7 + - - -
45C ARG 3.5 4.9 - - - -
46C GLU 3.2 0.2 - - - -
47C GLU* 1.3 75.6 - - - +
49C ILE* 1.3 58.0 + - - +
51C GLU* 3.3 5.6 + - - +
52C MET* 3.1 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 4.1 8.7 - - + -
45C ARG* 3.0 35.6 + - - +
46C GLU* 3.2 7.2 + - - +
48C SER* 1.3 73.2 - - - +
50C GLU* 1.3 65.0 + - - +
52C MET* 3.4 27.3 + - + +
53C GLY* 3.3 15.6 + - - -
202C HEM 4.0 46.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS* 4.9 8.0 + - - -
46C GLU* 2.9 19.9 + - + +
47C GLU* 3.1 16.7 + - - +
49C ILE* 1.3 77.5 - - - +
51C GLU* 1.3 63.5 + - - +
53C GLY* 3.0 17.7 + - - -
54C HIS* 3.1 27.0 + - + +
126C ASP* 5.3 4.9 - - - +
130C HIS* 2.9 31.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 2.5 46.7 - - - +
21C ALA* 3.8 19.3 - - + -
22C ILE* 3.5 23.4 - - + +
25C TYR* 3.9 11.9 - - + -
47C GLU 3.0 16.8 + - - +
48C SER 3.3 3.8 + - - +
50C GLU* 1.3 73.6 - - - +
52C MET* 1.3 65.7 + - - +
54C HIS* 3.0 17.6 + - - +
55C ALA* 2.8 24.1 + - - +
94C GLU* 6.0 0.4 - - - -
127C GLU* 3.5 9.9 - - - +
130C HIS* 3.3 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.5 22.4 - - + -
26C TRP* 3.7 13.2 - - + -
48C SER* 3.1 43.9 + - - +
49C ILE* 3.5 25.1 - - + +
50C GLU 3.2 0.2 - - - -
51C GLU* 1.3 74.7 - - - +
53C GLY* 1.3 63.7 + - - +
55C ALA* 3.3 3.2 + - - +
56C ASP* 3.0 23.9 + - - +
202C HEM 2.5 86.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE 3.3 6.0 + - - -
50C GLU 3.0 9.2 + - - -
52C MET* 1.3 77.3 - - - +
54C HIS* 1.3 65.8 + - - +
56C ASP* 3.3 7.4 + - - +
57C LYS* 3.0 26.8 + - - +
202C HEM 4.7 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 2.9 29.9 + - + +
50C GLU* 3.1 18.8 + - - +
51C GLU* 3.0 28.0 + - - +
53C GLY* 1.3 75.2 - - - +
55C ALA* 1.3 64.7 + - - +
57C LYS* 3.1 22.3 + - - +
58C ILE* 2.9 27.9 + - + +
123C LEU* 3.6 23.6 - - + +
126C ASP* 2.9 38.9 + - + -
127C GLU* 4.2 6.0 + - - -
130C HIS* 4.9 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 4.0 21.7 - - + +
18C GLU* 4.3 11.6 - - + +
19C LEU* 4.6 5.6 - - + -
22C ILE* 4.2 16.6 - - + -
51C GLU 2.8 12.1 + - - +
52C MET* 3.5 9.0 - - - +
54C HIS* 1.3 76.4 - - - +
56C ASP* 1.3 63.3 + - - +
58C ILE* 3.2 5.6 + - - +
59C ILE* 2.9 30.2 + - + +
202C HEM 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C MET 3.0 14.0 + - - +
53C GLY* 3.6 9.4 - - - +
54C HIS 3.3 0.2 - - - -
55C ALA* 1.3 75.0 - - - +
57C LYS* 1.3 65.2 + - - +
59C ILE* 3.2 13.0 + - - +
60C ALA* 3.0 25.2 + - - +
202C HEM 4.6 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLY 3.0 16.1 + - - +
54C HIS* 3.3 27.6 - - + +
56C ASP* 1.3 78.7 + - - +
58C ILE* 1.3 61.2 + - + +
60C ALA* 3.4 7.2 + - - +
61C ARG* 3.2 20.8 + - - +
119C ILE* 4.7 28.4 - - + +
122C SER* 4.3 16.6 + - - +
123C LEU* 5.7 5.6 - - + +
126C ASP* 5.1 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.5 34.5 - - + +
14C ALA* 3.9 20.0 - - + -
15C LEU* 4.0 13.0 - - + +
18C GLU* 4.3 16.2 - - + -
54C HIS* 2.9 19.2 + - - +
55C ALA* 3.2 5.8 + - - +
57C LYS* 1.3 76.8 - - + +
59C ILE* 1.3 66.0 + - - +
61C ARG* 3.3 7.1 + - - +
62C ILE* 3.0 28.1 + - + +
119C ILE* 4.7 12.1 - - + -
123C LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 3.9 23.8 - - + -
55C ALA* 2.9 25.2 + - + +
56C ASP* 3.2 11.4 + - - +
58C ILE* 1.3 76.5 - - - +
60C ALA* 1.3 62.4 + - - +
62C ILE* 3.3 8.5 + - - +
63C LEU* 3.1 32.4 + - + +
69C PRO* 3.8 22.2 - - + -
71C LEU* 3.8 31.4 - - + -
202C HEM 4.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP* 3.0 14.8 + - - +
57C LYS* 3.6 10.8 - - - +
59C ILE* 1.3 80.0 - - - +
61C ARG* 1.3 61.9 + - - +
63C LEU* 3.4 9.7 + - - +
64C PHE* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 2.9 31.5 + - - +
1C MET* 4.7 0.8 - - - +
11C LEU* 3.9 20.6 - - + -
57C LYS 3.2 11.9 + - - +
58C ILE* 3.3 9.8 + - - +
60C ALA* 1.3 79.3 - - - +
62C ILE* 1.3 63.2 + - - +
64C PHE* 3.3 21.5 + - - +
65C LEU* 3.1 39.1 + - + +
113C ASP* 2.9 31.9 + - - -
115C VAL* 3.4 22.8 - - - +
116C SER* 2.9 15.8 + - - +
119C ILE* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 4.6 9.4 - - + +
11C LEU* 3.5 38.1 - - + -
12C ASN* 3.7 30.7 - - - +
15C LEU* 4.5 4.7 - - + -
58C ILE* 3.0 23.9 + - + +
59C ILE* 3.5 7.2 - - - +
61C ARG* 1.3 76.7 - - - +
63C LEU* 1.3 63.3 + - - +
65C LEU* 3.1 11.2 + - - +
67C GLY* 2.9 37.9 + - - -
68C HIS 3.8 2.2 - - - +
69C PRO* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 3.1 31.7 + - + +
60C ALA* 3.8 7.4 - - - +
62C ILE* 1.3 76.4 - - - +
64C PHE* 1.3 58.7 + - - +
66C GLU* 2.8 23.2 + - - +
67C GLY 3.9 8.7 - - - +
68C HIS* 5.2 2.7 - - - +
69C PRO* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.5 27.6 - - + -
131A VAL* 4.3 3.1 - - + -
132A ASP* 3.3 54.7 - - + +
135A GLU* 3.6 16.1 - - - +
1C MET* 3.0 54.9 + - + +
60C ALA 3.0 16.8 + - - +
61C ARG* 3.4 36.6 - - - +
63C LEU* 1.3 78.5 - - - +
65C LEU* 1.3 62.9 + - + +
66C GLU* 3.1 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.1 26.2 - - + +
2C LYS* 4.1 1.2 - - - +
3C GLY* 3.0 37.8 + - - -
7C VAL* 4.0 7.9 - - + -
8C ILE* 3.5 18.7 - - + +
11C LEU* 3.8 28.9 - - + -
61C ARG* 3.1 38.2 + - - +
62C ILE 3.1 4.7 + - - +
64C PHE* 1.3 76.5 - - + +
66C GLU* 1.3 68.6 + - - +
67C GLY 3.3 1.4 + - - -
113C ASP* 3.9 9.2 - - - +
116C SER* 3.8 14.6 - - - +
----------------------------------------------------------
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